Stable version 0.7.0

This release is dedicated to RetroArch: the second best way to make your
PC feel like a 16bit system (right after building ShellCheck with GHC)

.compile_binaries

@@ -0,0 +1,82 @@
+#!/bin/bash
+
+_cleanup(){
+  rm -rf dist shellcheck || true
+}
+
+build_linux() {
+  # Linux Docker image
+  name="$DOCKER_BASE"
+  DOCKER_BUILDS="$DOCKER_BUILDS $name"
+  docker build -t "$name:current" .
+  docker run "$name:current" --version
+  printf '%s\n' "#!/bin/sh" "echo 'hello world'" > myscript
+  docker run -v "$PWD:/mnt" "$name:current" myscript
+
+  # Copy static executable from docker image
+  id=$(docker create "$name:current")
+  docker cp "$id:/bin/shellcheck" "shellcheck"
+  docker rm "$id"
+  ls -l shellcheck
+  ./shellcheck myscript
+  for tag in $TAGS
+  do 
+    cp "shellcheck" "deploy/shellcheck-$tag.linux-x86_64"; 
+  done
+
+  # Linux Alpine based Docker image
+  name="$DOCKER_BASE-alpine"
+  DOCKER_BUILDS="$DOCKER_BUILDS $name"
+  sed -e '/DELETE-MARKER/,$d' Dockerfile > Dockerfile.alpine
+  docker build -f Dockerfile.alpine -t "$name:current" .
+  docker run "$name:current" sh -c 'shellcheck --version'
+  _cleanup
+}
+
+build_aarch64() {
+  # Linux aarch64 static executable
+  docker run -v "$PWD:/mnt" koalaman/aarch64-builder 'buildsc'
+  for tag in $TAGS
+  do
+    cp "shellcheck" "deploy/shellcheck-$tag.linux-aarch64"
+  done
+}
+
+
+build_armv6hf() {
+  # Linux armv6hf static executable
+  docker run -v "$PWD:/mnt" koalaman/armv6hf-builder -c 'compile-shellcheck'
+  for tag in $TAGS
+  do 
+    cp "shellcheck" "deploy/shellcheck-$tag.linux-armv6hf"; 
+  done
+  _cleanup
+}
+
+build_windows() {
+  # Windows .exe
+  docker run --user="$UID" -v "$PWD:/appdata" koalaman/winghc cuib
+  for tag in $TAGS
+  do 
+    cp "dist/build/ShellCheck/shellcheck.exe" "deploy/shellcheck-$tag.exe"; 
+  done
+  _cleanup
+}
+
+build_osx() {
+  # Darwin x86_64 static executable
+  brew install cabal-install pandoc gnu-tar
+  sudo ln -s /usr/local/bin/gsha512sum /usr/local/bin/sha512sum
+  sudo ln -s /usr/local/bin/gtar /usr/local/bin/tar
+  export PATH="/usr/local/bin:$PATH"
+
+  cabal update
+  cabal install --dependencies-only
+  cabal build shellcheck
+  for tag in $TAGS
+  do 
+    cp "dist/build/shellcheck/shellcheck" "deploy/shellcheck-$tag.darwin-x86_64";
+  done
+  _cleanup
+}
+

.dockerignore

@@ -0,0 +1,6 @@
+*
+!LICENSE
+!Setup.hs
+!ShellCheck.cabal
+!shellcheck.hs
+!src

.github/ISSUE_TEMPLATE.md

@@ -1,7 +1,7 @@
 #### For bugs
 - Rule Id (if any, e.g. SC1000): 
 - My shellcheck version (`shellcheck --version` or "online"): 
-- [ ] I read the issue's wiki page, e.g. https://github.com/koalaman/shellcheck/wiki/SC2086
+- [ ] The rule's wiki page does not already cover this (e.g. https://shellcheck.net/wiki/SC2086)
 - [ ] I tried on shellcheck.net and verified that this is still a problem on the latest commit
 
 #### For new checks and feature suggestions

.prepare_deploy

@@ -35,6 +35,14 @@ do
   rm "shellcheck"
 done
 
+for file in *.linux-aarch64
+do
+  base="${file%.*}"
+  cp "$file" "shellcheck"
+  tar -cJf "$base.linux.aarch64.tar.xz" --transform="s:^:$base/:" README.txt LICENSE.txt shellcheck
+  rm "shellcheck"
+done
+
 for file in *.linux-armv6hf
 do
   base="${file%.*}"
@@ -43,8 +51,15 @@ do
   rm "shellcheck"
 done
 
+for file in *.darwin-x86_64
+do
+  base="${file%.*}"
+  cp "$file" "shellcheck"
+  tar -cJf "$base.darwin.x86_64.tar.xz" --transform="s:^:$base/:" README.txt LICENSE.txt shellcheck
+  rm "shellcheck"
+done
+
 for file in ./*
 do
   sha512sum "$file" > "$file.sha512sum"
 done
-

.snapsquid.conf

@@ -0,0 +1,14 @@
+# In 2015, cabal-install had a http bug triggered when proxies didn't keep
+# the connection open. This version made it into Ubuntu Xenial as used by
+# Snapcraft. In June 2018, Snapcraft's proxy started triggering this bug.
+#
+#     https://bugs.launchpad.net/launchpad-buildd/+bug/1797809
+#
+# Workaround: add more proxy
+
+visible_hostname localhost
+http_port 8888
+cache_peer 10.10.10.1 parent 8222 0 no-query default
+cache_peer_domain localhost !.internal
+http_access allow all
+

.travis.yml

@@ -1,3 +1,4 @@
+
 sudo: required
 
 language: sh
@@ -5,67 +6,52 @@ language: sh
 services:
   - docker
 
-before_install:
-  - DOCKER_BASE="$DOCKER_USERNAME/shellcheck"
-  - DOCKER_BUILDS=""
-  - TAGS=""
-  - test "$TRAVIS_BRANCH" = master && TAGS="$TAGS latest" || true
-  - test -n "$TRAVIS_TAG"          && TAGS="$TAGS stable $TRAVIS_TAG" || true
-  - echo "Tags are $TAGS"
+matrix:
+  include:
+    - os: linux
+      env: BUILD=linux
+    - os: linux
+      env: BUILD=windows
+    - os: linux
+      env: BUILD=armv6hf
+    - os: linux
+      env: BUILD=aarch64
+    - os: osx
+      env: BUILD=osx
+
+before_install: |
+  DOCKER_BASE="$DOCKER_USERNAME/shellcheck"
+  DOCKER_BUILDS=""
+  TAGS=""
+  test "$TRAVIS_BRANCH" = master && TAGS="$TAGS latest" || true
+  test -n "$TRAVIS_TAG"          && TAGS="$TAGS stable $TRAVIS_TAG" || true
+  echo "Tags are $TAGS"
 
 script:
-  - mkdir deploy
-  # Remove all tests to reduce binary size
+  - mkdir -p deploy
+  - source ./.compile_binaries
   - ./striptests
-  # Linux Docker image
-  - name="$DOCKER_BASE"
-  - DOCKER_BUILDS="$DOCKER_BUILDS $name"
-  - docker build -t "$name:current" .
-  - docker run "$name:current" --version
-  - printf '%s\n' "#!/bin/sh" "echo 'hello world'" > myscript
-  - docker run -v "$PWD:/mnt" "$name:current" myscript
-  # Copy static executable from docker image
-  - id=$(docker create "$name:current")
-  - docker cp "$id:/bin/shellcheck" "shellcheck"
-  - docker rm "$id"
-  - ls -l shellcheck
-  - ./shellcheck myscript
-  - for tag in $TAGS; do cp "shellcheck" "deploy/shellcheck-$tag.linux-x86_64"; done
-  # Linux Alpine based Docker image
-  - name="$DOCKER_BASE-alpine"
-  - DOCKER_BUILDS="$DOCKER_BUILDS $name"
-  - sed -e '/DELETE-MARKER/,$d' Dockerfile > Dockerfile.alpine
-  - docker build -f Dockerfile.alpine -t "$name:current" .
-  - docker run "$name:current" sh -c 'shellcheck --version'
-  # Linux armv6hf static executable
-  - docker run -v "$PWD:/mnt" koalaman/armv6hf-builder -c 'compile-shellcheck'
-  - for tag in $TAGS; do cp "shellcheck" "deploy/shellcheck-$tag.linux-armv6hf"; done
-  - rm -f shellcheck || true
-  # Windows .exe
-  - docker run --user="$UID" -v "$PWD:/appdata" koalaman/winghc cuib
-  - for tag in $TAGS; do cp "dist/build/ShellCheck/shellcheck.exe" "deploy/shellcheck-$tag.exe"; done
-  - rm -rf dist shellcheck || true
-  # Misc packaging
+  - set -x; build_"$BUILD"; set +x;
   - ./.prepare_deploy
 
-after_success:
-  - docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD"
-  - for repo in $DOCKER_BUILDS;
-    do
-      for tag in $TAGS;
-      do
+after_success: |
+  if [ "$BUILD" = "linux" ]; then
+    docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD"
+    for repo in $DOCKER_BUILDS; do
+      for tag in $TAGS; do
         echo "Deploying $repo:current as $repo:$tag...";
         docker tag "$repo:current" "$repo:$tag" || exit 1;
         docker push "$repo:$tag" || exit 1;
       done;
     done;
+  fi
 
-after_failure:
-  - id
-  - pwd
-  - df -h
-  - find . -name '*.log' -type f -exec grep "" /dev/null {} +
-  - find . -ls
+after_failure: |
+  id
+  pwd
+  df -h
+  find . -name '*.log' -type f -exec grep "" /dev/null {} +
+  find . -ls
 
 deploy:
   provider: gcs

CHANGELOG.md

@@ -1,17 +1,60 @@
-## ???
+## v0.7.0 - 2019-07-28
+### Added
+- Precompiled binaries for macOS and Linux aarch64
+- Preliminary support for fix suggestions
+- New `-f diff` unified diff format for auto-fixes
+- Files containing Bats tests can now be checked
+- Directory wide directives can now be placed in a `.shellcheckrc`
+- Optional checks: Use `--list-optional` to show a list of tests,
+                   Enable with `-o` flags or `enable=name` directives
+- Source paths: Use `-P dir1:dir2` or a `source-path=dir1` directive
+                to specify search paths for sourced files.
+- json1 format like --format=json but treats tabs as single characters
+- Recognize FLAGS variables created by the shflags library.
+- Site-specific changes can now be made in Custom.hs for ease of patching
+- SC2154: Also warn about unassigned uppercase variables (optional)
+- SC2252: Warn about `[ $a != x ] || [ $a != y ]`, similar to SC2055
+- SC2251: Inform about ineffectual ! in front of commands
+- SC2250: Warn about variable references without braces (optional)
+- SC2249: Warn about `case` with missing default case (optional)
+- SC2248: Warn about unquoted variables without special chars (optional)
+- SC2247: Warn about $"(cmd)" and $"{var}"
+- SC2246: Warn if a shebang's interpreter ends with /
+- SC2245: Warn that Ksh ignores all but the first glob result in `[`
+- SC2243/SC2244: Suggest using explicit -n for `[ $foo ]` (optional)
+- SC1135: Suggest not ending double quotes just to make $ literal
+
+### Changed
+- If a directive or shebang is not specified, a `.bash/.bats/.dash/.ksh`
+  extension will be used to infer the shell type when present.
+- Disabling SC2120 on a function now disables SC2119 on call sites
+
+### Fixed
+- SC2183 no longer warns about missing printf args for `%()T`
+
+## v0.6.0 - 2018-12-02
 ### Added
 - Command line option --severity/-S for filtering by minimum severity
 - Command line option --wiki-link-count/-W for showing wiki links
+- SC2152/SC2151: Warn about bad `exit` values like `1234` and `"foo"`
 - SC2236/SC2237: Suggest -n/-z instead of ! -z/-n
 - SC2238: Warn when redirecting to a known command name, e.g. ls > rm
 - SC2239: Warn if the shebang is not an absolute path, e.g. #!bin/sh
+- SC2240: Warn when passing additional arguments to dot (.) in sh/dash
 - SC1133: Better diagnostics when starting a line with |/||/&&
+
 ### Changed
 - Most warnings now have useful end positions
 - SC1117 about unknown double-quoted escape sequences has been retired
+
 ### Fixed
-- SC2021 no longer triggers for equivalence classes like '[=e=]'
+- SC2021 no longer triggers for equivalence classes like `[=e=]`
 - SC2221/SC2222 no longer mistriggers on fall-through case branches
+- SC2081 about glob matches in `[ .. ]` now also triggers for `!=`
+- SC2086 no longer warns about spaces in `$#`
+- SC2164 no longer suggests subshells for `cd ..; cmd; cd ..`
+- `read -a` is now correctly considered an array assignment
+- SC2039 no longer warns about LINENO now that it's POSIX
 
 ## v0.5.0 - 2018-05-31
 ### Added

Dockerfile

@@ -1,5 +1,5 @@
 # Build-only image
-FROM ubuntu:17.10 AS build
+FROM ubuntu:18.04 AS build
 USER root
 WORKDIR /opt/shellCheck
 

README.md

@@ -8,45 +8,45 @@ ShellCheck is a GPLv3 tool that gives warnings and suggestions for bash/sh shell
 
 The goals of ShellCheck are
 
-- To point out and clarify typical beginner's syntax issues that cause a shell
+* To point out and clarify typical beginner's syntax issues that cause a shell
   to give cryptic error messages.
 
-- To point out and clarify typical intermediate level semantic problems that
+* To point out and clarify typical intermediate level semantic problems that
   cause a shell to behave strangely and counter-intuitively.
 
-- To point out subtle caveats, corner cases and pitfalls that may cause an
+* To point out subtle caveats, corner cases and pitfalls that may cause an
   advanced user's otherwise working script to fail under future circumstances.
 
 See [the gallery of bad code](README.md#user-content-gallery-of-bad-code) for examples of what ShellCheck can help you identify!
 
 ## Table of Contents
 
-- [How to use](#how-to-use)
-  - [On the web](#on-the-web)
-  - [From your terminal](#from-your-terminal)
-  - [In your editor](#in-your-editor)
-  - [In your build or test suites](#in-your-build-or-test-suites)
-- [Installing](#installing)
-- [Travis CI](#travis-ci)
-- [Compiling from source](#compiling-from-source)
-  - [Installing Cabal](#installing-cabal)
-  - [Compiling ShellCheck](#compiling-shellcheck)
-  - [Running tests](#running-tests)
-- [Gallery of bad code](#gallery-of-bad-code)
-  - [Quoting](#quoting)
-  - [Conditionals](#conditionals)
-  - [Frequently misused commands](#frequently-misused-commands)
-  - [Common beginner's mistakes](#common-beginners-mistakes)
-  - [Style](#style)
-  - [Data and typing errors](#data-and-typing-errors)
-  - [Robustness](#robustness)
-  - [Portability](#portability)
-  - [Miscellaneous](#miscellaneous)
-- [Testimonials](#testimonials)
-- [Ignoring issues](#ignoring-issues)
-- [Reporting bugs](#reporting-bugs)
-- [Contributing](#contributing)
-- [Copyright](#copyright)
+* [How to use](#how-to-use)
+  * [On the web](#on-the-web)
+  * [From your terminal](#from-your-terminal)
+  * [In your editor](#in-your-editor)
+  * [In your build or test suites](#in-your-build-or-test-suites)
+* [Installing](#installing)
+* [Compiling from source](#compiling-from-source)
+  * [Installing Cabal](#installing-cabal)
+  * [Compiling ShellCheck](#compiling-shellcheck)
+  * [Running tests](#running-tests)
+* [Gallery of bad code](#gallery-of-bad-code)
+  * [Quoting](#quoting)
+  * [Conditionals](#conditionals)
+  * [Frequently misused commands](#frequently-misused-commands)
+  * [Common beginner's mistakes](#common-beginners-mistakes)
+  * [Style](#style)
+  * [Data and typing errors](#data-and-typing-errors)
+  * [Robustness](#robustness)
+  * [Portability](#portability)
+  * [Miscellaneous](#miscellaneous)
+* [Testimonials](#testimonials)
+* [Ignoring issues](#ignoring-issues)
+* [Reporting bugs](#reporting-bugs)
+* [Contributing](#contributing)
+* [Copyright](#copyright)
+* [Other Resources](#other-resources)
 
 ## How to use
 
@@ -54,7 +54,7 @@ There are a number of ways to use ShellCheck!
 
 ### On the web
 
-Paste a shell script on https://www.shellcheck.net for instant feedback.
+Paste a shell script on <https://www.shellcheck.net> for instant feedback.
 
 [ShellCheck.net](https://www.shellcheck.net) is always synchronized to the latest git commit, and is the easiest way to give ShellCheck a go. Tell your friends!
 
@@ -85,8 +85,45 @@ You can see ShellCheck suggestions directly in a variety of editors.
 ### In your build or test suites
 
 While ShellCheck is mostly intended for interactive use, it can easily be added to builds or test suites.
+It makes canonical use of exit codes, so you can just add a `shellcheck` command as part of the process.
 
-ShellCheck makes canonical use of exit codes, and can output simple JSON, CheckStyle compatible XML, GCC compatible warnings as well as human readable text (with or without ANSI colors). See the [Integration](https://github.com/koalaman/shellcheck/wiki/Integration) wiki page for more documentation.
+For example, in a Makefile:
+
+```Makefile
+check-scripts:
+    # Fail if any of these files have warnings
+    shellcheck myscripts/*.sh
+```
+
+or in a Travis CI `.travis.yml` file:
+
+```yaml
+script:
+  # Fail if any of these files have warnings
+  - shellcheck myscripts/*.sh
+```
+
+Services and platforms that have ShellCheck pre-installed and ready to use:
+
+* [Travis CI](https://travis-ci.org/)
+* [Codacy](https://www.codacy.com/)
+* [Code Climate](https://codeclimate.com/)
+* [Code Factor](https://www.codefactor.io/)
+
+Services and platforms with third party plugins:
+
+* [SonarQube](https://www.sonarqube.org/) through [sonar-shellcheck-plugin](https://github.com/emerald-squad/sonar-shellcheck-plugin)
+
+Most other services, including [GitLab](https://about.gitlab.com/), let you install
+ShellCheck yourself, either through the system's package manager (see [Installing](#installing)),
+or by downloading and unpacking a [binary release](#installing-the-shellcheck-binary).
+
+It's a good idea to manually install a specific ShellCheck version regardless. This avoids
+any surprise build breaks when a new version with new warnings is published.
+
+For customized filtering or reporting, ShellCheck can output simple JSON, CheckStyle compatible XML,
+GCC compatible warnings as well as human readable text (with or without ANSI colors). See the
+[Integration](https://github.com/koalaman/shellcheck/wiki/Integration) wiki page for more documentation.
 
 ## Installing
 
@@ -133,19 +170,31 @@ On OS X with homebrew:
 
     brew install shellcheck
 
+On OpenBSD:
+
+    pkg_add shellcheck
+
 On openSUSE
 
     zypper in ShellCheck
 
-Or use OneClickInstall - https://software.opensuse.org/package/ShellCheck
+Or use OneClickInstall - <https://software.opensuse.org/package/ShellCheck>
 
 On Solus:
 
     eopkg install shellcheck
-    
-On Windows (via [scoop](http://scoop.sh)):
 
-    scoop install shellcheck
+On Windows (via [chocolatey](https://chocolatey.org/packages/shellcheck)):
+
+```cmd
+C:\> choco install shellcheck
+```
+
+Or Windows (via [scoop](http://scoop.sh)):
+
+```cmd
+C:\> scoop install shellcheck
+```
 
 From Snap Store:
 
@@ -154,8 +203,8 @@ From Snap Store:
 From Docker Hub:
 
 ```sh
-docker pull koalaman/shellcheck:stable  # Or :v0.4.7 for that version, or :latest for daily builds
-docker run -v "$PWD:/mnt" koalaman/shellcheck myscript
+docker run --rm -v "$PWD:/mnt" koalaman/shellcheck:stable myscript
+# Or :v0.4.7 for that version, or :latest for daily builds
 ```
 
 or use `koalaman/shellcheck-alpine` if you want a larger Alpine Linux based image to extend. It works exactly like a regular Alpine image, but has shellcheck preinstalled.
@@ -164,27 +213,39 @@ Alternatively, you can download pre-compiled binaries for the latest release her
 
 * [Linux, x86_64](https://storage.googleapis.com/shellcheck/shellcheck-stable.linux.x86_64.tar.xz) (statically linked)
 * [Linux, armv6hf](https://storage.googleapis.com/shellcheck/shellcheck-stable.linux.armv6hf.tar.xz), i.e. Raspberry Pi (statically linked)
+* [Linux, aarch64](https://storage.googleapis.com/shellcheck/shellcheck-stable.linux.armv6hf.tar.xz) aka ARM64 (statically linked)
+* [MacOS, x86_64](https://shellcheck.storage.googleapis.com/shellcheck-stable.darwin.x86_64.tar.xz)
 * [Windows, x86](https://storage.googleapis.com/shellcheck/shellcheck-stable.zip)
 
 or see the [storage bucket listing](https://shellcheck.storage.googleapis.com/index.html) for checksums, older versions and the latest daily builds.
 
-## Travis CI
+Distro packages already come with a `man` page. If you are building from source, it can be installed with:
+
+```console
+pandoc -s -f markdown-smart -t man shellcheck.1.md -o shellcheck.1
+sudo mv shellcheck.1 /usr/share/man/man1
+```
+
+### Travis CI
 
 Travis CI has now integrated ShellCheck by default, so you don't need to manually install it.
 
-If you still want to do so in order to upgrade at your leisure or ensure the latest release, follow the steps to install the shellcheck binary, bellow.
+If you still want to do so in order to upgrade at your leisure or ensure you're
+using the latest release, follow the steps below to install a binary version.
 
-## Installing the shellcheck binary
+### Installing a pre-compiled binary
 
-*Pre-requisite*: the program 'xz' needs to be installed on the system.  
-To install it on debian/ubuntu/linux mint, run `apt install xz-utils`.  
-To install it on Redhat/Fedora/CentOS, run `yum -y install xz`.  
+The pre-compiled binaries come in `tar.xz` files. To decompress them, make sure
+`xz` is installed.
+On Debian/Ubuntu/Mint, you can `apt install xz-utils`.
+On Redhat/Fedora/CentOS, `yum -y install xz`.
+
+A simple installer may do something like:
 
 ```bash
-export scversion="stable" # or "v0.4.7", or "latest"
-wget "https://storage.googleapis.com/shellcheck/shellcheck-${scversion}.linux.x86_64.tar.xz"
-tar --xz -xvf shellcheck-"${scversion}".linux.x86_64.tar.xz
-cp shellcheck-"${scversion}"/shellcheck /usr/bin/
+scversion="stable" # or "v0.4.7", or "latest"
+wget -qO- "https://storage.googleapis.com/shellcheck/shellcheck-${scversion?}.linux.x86_64.tar.xz" | tar -xJv
+cp "shellcheck-${scversion}/shellcheck" /usr/bin/
 shellcheck --version
 ```
 
@@ -198,11 +259,9 @@ ShellCheck is built and packaged using Cabal. Install the package `cabal-install
 
 On MacOS (OS X), you can do a fast install of Cabal using brew, which takes a couple of minutes instead of more than 30 minutes if you try to compile it from source.
 
-    brew install cask
-    brew cask install haskell-platform
-    cabal install cabal-install
+    $ brew install cabal-install
 
-On MacPorts, the package is instead called `hs-cabal-install`, while native Windows users should install the latest version of the Haskell platform from https://www.haskell.org/platform/
+On MacPorts, the package is instead called `hs-cabal-install`, while native Windows users should install the latest version of the Haskell platform from <https://www.haskell.org/platform/>
 
 Verify that `cabal` is installed and update its dependency list with
 
@@ -238,12 +297,15 @@ may use a legacy codepage. In `cmd.exe`, `powershell.exe` and Powershell ISE,
 make sure to use a TrueType font, not a Raster font, and set the active
 codepage to UTF-8 (65001) with `chcp`:
 
-    > chcp 65001
-    Active code page: 65001
+```cmd
+chcp 65001
+```
 
 In Powershell ISE, you may need to additionally update the output encoding:
 
-    > [Console]::OutputEncoding = [System.Text.Encoding]::UTF8
+```powershell
+[Console]::OutputEncoding = [System.Text.Encoding]::UTF8
+```
 
 ### Running tests
 
@@ -421,13 +483,13 @@ Alexander Tarasikov,
 
 Issues can be ignored via environmental variable, command line, individually or globally within a file:
 
-https://github.com/koalaman/shellcheck/wiki/Ignore
+<https://github.com/koalaman/shellcheck/wiki/Ignore>
 
 ## Reporting bugs
 
 Please use the GitHub issue tracker for any bugs or feature suggestions:
 
-https://github.com/koalaman/shellcheck/issues
+<https://github.com/koalaman/shellcheck/issues>
 
 ## Contributing
 
@@ -442,11 +504,12 @@ The contributor retains the copyright.
 
 ShellCheck is licensed under the GNU General Public License, v3. A copy of this license is included in the file [LICENSE](LICENSE).
 
-Copyright 2012-2018, Vidar 'koala_man' Holen and contributors.
+Copyright 2012-2019, [Vidar 'koala_man' Holen](https://github.com/koalaman/) and contributors.
 
 Happy ShellChecking!
 
+## Other Resources
 
-## Other Resources                                                                          
 * The wiki has [long form descriptions](https://github.com/koalaman/shellcheck/wiki/Checks) for each warning, e.g. [SC2221](https://github.com/koalaman/shellcheck/wiki/SC2221).
 * ShellCheck does not attempt to enforce any kind of formatting or indenting style, so also check out [shfmt](https://github.com/mvdan/sh)!
+

Setup.hs

@@ -33,4 +33,4 @@ myPreSDist _ _ = do
   putStrLn $ "pandoc exited with " ++ show result
   return emptyHookedBuildInfo
   where
-    pandoc_cmd = "pandoc -s -t man shellcheck.1.md -o shellcheck.1"
+    pandoc_cmd = "pandoc -s -f markdown-smart -t man shellcheck.1.md -o shellcheck.1"

ShellCheck.cabal

@@ -1,5 +1,5 @@
 Name:             ShellCheck
-Version:          0.5.0
+Version:          0.7.0
 Synopsis:         Shell script analysis tool
 License:          GPL-3
 License-file:     LICENSE
@@ -28,6 +28,8 @@ Extra-Source-Files:
     shellcheck.1.md
     -- built with a cabal sdist hook
     shellcheck.1
+    -- convenience script for stripping tests
+    striptests
     -- tests
     test/shellcheck.hs
 
@@ -47,15 +49,18 @@ library
       build-depends:
         semigroups
     build-depends:
+      aeson,
+      array,
       -- GHC 7.6.3 (base 4.6.0.1) is buggy (#1131, #1119) in optimized mode.
       -- Just disable that version entirely to fail fast.
-      aeson,
       base > 4.6.0.1 && < 5,
       bytestring,
       containers >= 0.5,
       deepseq >= 1.4.0.0,
-      directory,
+      Diff >= 0.2.0,
+      directory >= 1.2.3.0,
       mtl >= 2.2.1,
+      filepath,
       parsec,
       regex-tdfa,
       QuickCheck >= 2.7.4,
@@ -69,13 +74,18 @@ library
       ShellCheck.AnalyzerLib
       ShellCheck.Checker
       ShellCheck.Checks.Commands
+      ShellCheck.Checks.Custom
       ShellCheck.Checks.ShellSupport
       ShellCheck.Data
+      ShellCheck.Fixer
       ShellCheck.Formatter.Format
       ShellCheck.Formatter.CheckStyle
+      ShellCheck.Formatter.Diff
       ShellCheck.Formatter.GCC
       ShellCheck.Formatter.JSON
+      ShellCheck.Formatter.JSON1
       ShellCheck.Formatter.TTY
+      ShellCheck.Formatter.Quiet
       ShellCheck.Interface
       ShellCheck.Parser
       ShellCheck.Regex
@@ -88,31 +98,37 @@ executable shellcheck
         semigroups
     build-depends:
       aeson,
+      array,
       base >= 4 && < 5,
       bytestring,
-      deepseq >= 1.4.0.0,
-      ShellCheck,
       containers,
-      directory,
+      deepseq >= 1.4.0.0,
+      Diff >= 0.2.0,
+      directory >= 1.2.3.0,
       mtl >= 2.2.1,
+      filepath,
       parsec >= 3.0,
       QuickCheck >= 2.7.4,
-      regex-tdfa
+      regex-tdfa,
+      ShellCheck
     main-is: shellcheck.hs
 
 test-suite test-shellcheck
     type: exitcode-stdio-1.0
     build-depends:
       aeson,
+      array,
       base >= 4 && < 5,
       bytestring,
-      deepseq >= 1.4.0.0,
-      ShellCheck,
       containers,
-      directory,
+      deepseq >= 1.4.0.0,
+      Diff >= 0.2.0,
+      directory >= 1.2.3.0,
       mtl >= 2.2.1,
+      filepath,
       parsec,
       QuickCheck >= 2.7.4,
-      regex-tdfa
+      regex-tdfa,
+      ShellCheck
     main-is: test/shellcheck.hs
 

quicktest

@@ -4,15 +4,8 @@
 # 'cabal test' remains the source of truth.
 
 (
- var=$(echo 'liftM and $ sequence [
-  ShellCheck.Analytics.runTests
-  ,ShellCheck.Parser.runTests
-  ,ShellCheck.Checker.runTests
-  ,ShellCheck.Checks.Commands.runTests
-  ,ShellCheck.Checks.ShellSupport.runTests
-  ,ShellCheck.AnalyzerLib.runTests
-    ]' | tr -d '\n' | cabal repl 2>&1 | tee /dev/stderr)
-if [[ $var == *$'\nTrue'* ]]
+var=$(echo 'main' | ghci test/shellcheck.hs 2>&1 | tee /dev/stderr)
+if [[ $var == *ExitSuccess* ]]
 then
   exit 0
 else

shellcheck.1.md

@@ -29,14 +29,13 @@ will warn that decimals are not supported.
 + For scripts starting with `#!/bin/ksh` (or using `-s ksh`), ShellCheck will
 not warn at all, as `ksh` supports decimals in arithmetic contexts.
 
-
 # OPTIONS
 
 **-a**,\ **--check-sourced**
 
 :   Emit warnings in sourced files. Normally, `shellcheck` will only warn
     about issues in the specified files. With this option, any issues in
-    sourced files files will also be reported.
+    sourced files will also be reported.
 
 **-C**[*WHEN*],\ **--color**[=*WHEN*]
 
@@ -44,6 +43,13 @@ not warn at all, as `ksh` supports decimals in arithmetic contexts.
     is *auto*. **--color** without an argument is equivalent to
     **--color=always**.
 
+**-i**\ *CODE1*[,*CODE2*...],\ **--include=***CODE1*[,*CODE2*...]
+
+:   Explicitly include only the specified codes in the report. Subsequent **-i**
+    options are cumulative, but all the codes can be specified at once,
+    comma-separated as a single argument. Include options override any provided
+    exclude options.
+
 **-e**\ *CODE1*[,*CODE2*...],\ **--exclude=***CODE1*[,*CODE2*...]
 
 :   Explicitly exclude the specified codes from the report. Subsequent **-e**
@@ -56,16 +62,39 @@ not warn at all, as `ksh` supports decimals in arithmetic contexts.
     standard output. Subsequent **-f** options are ignored, see **FORMATS**
     below for more information.
 
-**-S**\ *SEVERITY*,\ **--severity=***severity*
+**--list-optional**
 
-:   Specify minimum severity of errors to consider. Valid values are *error*,
-    *warning*, *info* and *style*.    The default is *style*.
+:   Output a list of known optional checks. These can be enabled with **-o**
+    flags or **enable** directives.
+
+**--norc**
+
+:   Don't try to look for .shellcheckrc configuration files.
+
+**-o**\ *NAME1*[,*NAME2*...],\ **--enable=***NAME1*[,*NAME2*...]
+
+:   Enable optional checks. The special name *all* enables all of them.
+    Subsequent **-o** options accumulate. This is equivalent to specifying
+    **enable** directives.
+
+**-P**\ *SOURCEPATH*,\ **--source-path=***SOURCEPATH*
+
+:   Specify paths to search for sourced files, separated by `:` on Unix and
+    `;` on Windows. This is equivalent to specifying `search-path`
+    directives.
 
 **-s**\ *shell*,\ **--shell=***shell*
 
 :   Specify Bourne shell dialect. Valid values are *sh*, *bash*, *dash* and *ksh*.
-    The default is to use the file's shebang, or *bash* if the target shell
-    can't be determined.
+    The default is to deduce the shell from the file's `shell` directive,
+    shebang, or `.bash/.bats/.dash/.ksh` extension, in that order. *sh* refers to
+    POSIX `sh` (not the system's), and will warn of portability issues.
+
+**-S**\ *SEVERITY*,\ **--severity=***severity*
+
+:   Specify minimum severity of errors to consider. Valid values in order of
+    severity are *error*, *warning*, *info* and *style*.
+    The default is *style*.
 
 **-V**,\ **--version**
 
@@ -83,6 +112,10 @@ not warn at all, as `ksh` supports decimals in arithmetic contexts.
     line (plus `/dev/null`). This option allows following any file the script
     may `source`.
 
+**FILES...**
+
+:   One or more script files to check, or "-" for standard input.
+
 
 # FORMATS
 
@@ -119,27 +152,59 @@ not warn at all, as `ksh` supports decimals in arithmetic contexts.
           ...
         </checkstyle>
 
-**json**
+**diff**
+
+:   Auto-fixes in unified diff format. Can be piped to `git apply` or `patch -p1`
+    to automatically apply fixes.
+
+        --- a/test.sh
+        +++ b/test.sh
+        @@ -2,6 +2,6 @@
+         ## Example of a broken script.
+         for f in $(ls *.m3u)
+         do
+        -  grep -qi hq.*mp3 $f \
+        +  grep -qi hq.*mp3 "$f" \
+             && echo -e 'Playlist $f contains a HQ file in mp3 format'
+         done
+
+
+**json1**
 
 :   Json is a popular serialization format that is more suitable for web
     applications. ShellCheck's json is compact and contains only the bare
-    minimum.
+    minimum.  Tabs are counted as 1 character.
+
+        {
+          comments: [
+            {
+              "file": "filename",
+              "line": lineNumber,
+              "column": columnNumber,
+              "level": "severitylevel",
+              "code": errorCode,
+              "message": "warning message"
+            },
+            ...
+          ]
+        }
+
+**json**
+
+:   This is a legacy version of the **json1** format. It's a raw array of
+    comments, and all offsets have a tab stop of 8.
+
+**quiet**
+
+:   Suppress all normal output. Exit with zero if no issues are found,
+    otherwise exit with one. Stops processing after the first issue.
 
-        [
-          {
-            "file": "filename",
-            "line": lineNumber,
-            "column": columnNumber,
-            "level": "severitylevel",
-            "code": errorCode,
-            "message": "warning message"
-          },
-          ...
-        ]
 
 # DIRECTIVES
-ShellCheck directives can be specified as comments in the shell script
-before a command or block:
+
+ShellCheck directives can be specified as comments in the shell script.
+If they appear before the first command, they are considered file-wide.
+Otherwise, they apply to the immediately following command or block:
 
     # shellcheck key=value key=value
     command-or-structure
@@ -169,17 +234,64 @@ Valid keys are:
     The command can be a simple command like `echo foo`, or a compound command
     like a function definition, subshell block or loop.
 
+**enable**
+:   Enable an optional check by name, as listed with **--list-optional**.
+    Only file-wide `enable` directives are considered.
+
 **source**
 :   Overrides the filename included by a `source`/`.` statement. This can be
     used to tell shellcheck where to look for a file whose name is determined
     at runtime, or to skip a source by telling it to use `/dev/null`.
 
+**source-path**
+:   Add a directory to the search path for `source`/`.` statements (by default,
+    only ShellCheck's working directory is included). Absolute paths will also
+    be rooted in these paths. The special path `SCRIPTDIR` can be used to
+    specify the currently checked script's directory, as in
+    `source-path=SCRIPTDIR` or `source-path=SCRIPTDIR/../libs`. Multiple
+    paths accumulate, and `-P` takes precedence over them.
+
 **shell**
 :   Overrides the shell detected from the shebang.  This is useful for
     files meant to be included (and thus lacking a shebang), or possibly
     as a more targeted alternative to 'disable=2039'.
 
+# RC FILES
+
+Unless `--norc` is used, ShellCheck will look for a file `.shellcheckrc` or
+`shellcheckrc` in the script's directory and each parent directory. If found,
+it will read `key=value` pairs from it and treat them as file-wide directives.
+
+Here is an example `.shellcheckrc`:
+
+    # Look for 'source'd files relative to the checked script,
+    # and also look for absolute paths in /mnt/chroot
+    source-path=SCRIPTDIR
+    source-path=/mnt/chroot
+
+    # Turn on warnings for unquoted variables with safe values
+    enable=quote-safe-variables
+
+    # Turn on warnings for unassigned uppercase variables
+    enable=check-unassigned-uppercase
+
+    # Allow using `which` since it gives full paths and is common enough
+    disable=SC2230
+
+If no `.shellcheckrc` is found in any of the parent directories, ShellCheck
+will look in `~/.shellcheckrc` followed by the XDG config directory
+(usually `~/.config/shellcheckrc`) on Unix, or `%APPDATA%/shellcheckrc` on
+Windows. Only the first file found will be used.
+
+Note for Snap users: the Snap sandbox disallows access to hidden files.
+Use `shellcheckrc` without the dot instead.
+
+Note for Docker users: ShellCheck will only be able to look for files that
+are mounted in the container, so `~/.shellcheckrc` will not be read.
+
+
 # ENVIRONMENT VARIABLES
+
 The environment variable `SHELLCHECK_OPTS` can be set with default flags:
 
     export SHELLCHECK_OPTS='--shell=bash --exclude=SC2016'
@@ -198,6 +310,7 @@ ShellCheck uses the follow exit codes:
 + 4: ShellCheck was invoked with bad options (e.g. unknown formatter).
 
 # LOCALE
+
 This version of ShellCheck is only available in English. All files are
 leniently decoded as UTF-8, with a fallback of ISO-8859-1 for invalid
 sequences. `LC_CTYPE` is respected for output, and defaults to UTF-8 for
@@ -206,20 +319,23 @@ locales where encoding is unspecified (such as the `C` locale).
 Windows users seeing `commitBuffer: invalid argument (invalid character)`
 should set their terminal to use UTF-8 with `chcp 65001`.
 
-# AUTHOR
-ShellCheck is written and maintained by Vidar Holen.
+# AUTHORS
+
+ShellCheck is developed and maintained by Vidar Holen, with assistance from a
+long list of wonderful contributors.
 
 # REPORTING BUGS
+
 Bugs and issues can be reported on GitHub:
 
 https://github.com/koalaman/shellcheck/issues
 
 # COPYRIGHT
-Copyright 2012-2015, Vidar Holen.
+
+Copyright 2012-2019, Vidar Holen and contributors.
 Licensed under the GNU General Public License version 3 or later,
 see https://gnu.org/licenses/gpl.html
 
-
 # SEE ALSO
 
 sh(1) bash(1)

shellcheck.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -17,6 +17,7 @@
     You should have received a copy of the GNU General Public License
     along with this program.  If not, see <https://www.gnu.org/licenses/>.
 -}
+import qualified ShellCheck.Analyzer
 import           ShellCheck.Checker
 import           ShellCheck.Data
 import           ShellCheck.Interface
@@ -24,9 +25,12 @@ import           ShellCheck.Regex
 
 import qualified ShellCheck.Formatter.CheckStyle
 import           ShellCheck.Formatter.Format
+import qualified ShellCheck.Formatter.Diff
 import qualified ShellCheck.Formatter.GCC
 import qualified ShellCheck.Formatter.JSON
+import qualified ShellCheck.Formatter.JSON1
 import qualified ShellCheck.Formatter.TTY
+import qualified ShellCheck.Formatter.Quiet
 
 import           Control.Exception
 import           Control.Monad
@@ -46,6 +50,7 @@ import           System.Console.GetOpt
 import           System.Directory
 import           System.Environment
 import           System.Exit
+import           System.FilePath
 import           System.IO
 
 data Flag = Flag String String
@@ -67,6 +72,7 @@ instance Monoid Status where
 data Options = Options {
     checkSpec        :: CheckSpec,
     externalSources  :: Bool,
+    sourcePaths      :: [FilePath],
     formatterOptions :: FormatterOptions,
     minSeverity      :: Severity
 }
@@ -74,6 +80,7 @@ data Options = Options {
 defaultOptions = Options {
     checkSpec = emptyCheckSpec,
     externalSources = False,
+    sourcePaths = [],
     formatterOptions = newFormatterOptions {
         foColorOption = ColorAuto
     },
@@ -87,11 +94,23 @@ options = [
     Option "C" ["color"]
         (OptArg (maybe (Flag "color" "always") (Flag "color")) "WHEN")
         "Use color (auto, always, never)",
+    Option "i" ["include"]
+        (ReqArg (Flag "include") "CODE1,CODE2..") "Consider only given types of warnings",
     Option "e" ["exclude"]
         (ReqArg (Flag "exclude") "CODE1,CODE2..") "Exclude types of warnings",
     Option "f" ["format"]
         (ReqArg (Flag "format") "FORMAT") $
         "Output format (" ++ formatList ++ ")",
+    Option "" ["list-optional"]
+        (NoArg $ Flag "list-optional" "true") "List checks disabled by default",
+    Option "" ["norc"]
+        (NoArg $ Flag "norc" "true") "Don't look for .shellcheckrc files",
+    Option "o" ["enable"]
+        (ReqArg (Flag "enable") "check1,check2..")
+        "List of optional checks to enable (or 'all')",
+    Option "P" ["source-path"]
+        (ReqArg (Flag "source-path") "SOURCEPATHS")
+        "Specify path when looking for sourced files (\"SCRIPTDIR\" for script's dir)",
     Option "s" ["shell"]
         (ReqArg (Flag "shell") "SHELLNAME")
         "Specify dialect (sh, bash, dash, ksh)",
@@ -102,10 +121,13 @@ options = [
         (NoArg $ Flag "version" "true") "Print version information",
     Option "W" ["wiki-link-count"]
         (ReqArg (Flag "wiki-link-count") "NUM")
-        "The number of wiki links to show, when applicable.",
+        "The number of wiki links to show, when applicable",
     Option "x" ["external-sources"]
-        (NoArg $ Flag "externals" "true") "Allow 'source' outside of FILES"
+        (NoArg $ Flag "externals" "true") "Allow 'source' outside of FILES",
+    Option "" ["help"]
+        (NoArg $ Flag "help" "true") "Show this usage summary and exit"
     ]
+getUsageInfo = usageInfo usageHeader options
 
 printErr = lift . hPutStrLn stderr
 
@@ -114,15 +136,18 @@ parseArguments argv =
     case getOpt Permute options argv of
         (opts, files, []) -> return (opts, files)
         (_, _, errors) -> do
-            printErr $ concat errors ++ "\n" ++ usageInfo usageHeader options
+            printErr $ concat errors ++ "\n" ++ getUsageInfo
             throwError SyntaxFailure
 
 formats :: FormatterOptions -> Map.Map String (IO Formatter)
 formats options = Map.fromList [
     ("checkstyle", ShellCheck.Formatter.CheckStyle.format),
+    ("diff",  ShellCheck.Formatter.Diff.format options),
     ("gcc",  ShellCheck.Formatter.GCC.format),
     ("json", ShellCheck.Formatter.JSON.format),
-    ("tty",  ShellCheck.Formatter.TTY.format options)
+    ("json1", ShellCheck.Formatter.JSON1.format),
+    ("tty",  ShellCheck.Formatter.TTY.format options),
+    ("quiet",  ShellCheck.Formatter.Quiet.format options)
     ]
 
 formatList = intercalate ", " names
@@ -267,10 +292,30 @@ parseOption flag options =
                 }
             }
 
+        Flag "include" str -> do
+            new <- mapM parseNum $ filter (not . null) $ split ',' str
+            let old = csIncludedWarnings . checkSpec $ options
+            return options {
+                checkSpec = (checkSpec options) {
+                    csIncludedWarnings =
+                      if null new
+                        then old
+                        else Just new `mappend` old
+                }
+            }
+
         Flag "version" _ -> do
             liftIO printVersion
             throwError NoProblems
 
+        Flag "list-optional" _ -> do
+            liftIO printOptional
+            throwError NoProblems
+
+        Flag "help" _ -> do
+            liftIO $ putStrLn getUsageInfo
+            throwError NoProblems
+
         Flag "externals" _ ->
             return options {
                 externalSources = True
@@ -284,6 +329,12 @@ parseOption flag options =
                 }
             }
 
+        Flag "source-path" str -> do
+            let paths = splitSearchPath str
+            return options {
+                sourcePaths = (sourcePaths options) ++ paths
+            }
+
         Flag "sourced" _ ->
             return options {
                 checkSpec = (checkSpec options) {
@@ -307,7 +358,26 @@ parseOption flag options =
                 }
             }
 
-        _ -> return options
+        Flag "norc" _ ->
+            return options {
+                checkSpec = (checkSpec options) {
+                    csIgnoreRC = True
+                }
+            }
+
+        Flag "enable" value ->
+            let cs = checkSpec options in return options {
+                checkSpec = cs {
+                    csOptionalChecks = (csOptionalChecks cs) ++ split ',' value
+                }
+            }
+
+        -- This flag is handled specially in 'process'
+        Flag "format" _ -> return options
+
+        Flag str _ -> do
+            printErr $ "Internal error for --" ++ str ++ ". Please file a bug :("
+            return options
   where
     die s = do
         printErr s
@@ -322,12 +392,16 @@ parseOption flag options =
 ioInterface options files = do
     inputs <- mapM normalize files
     cache <- newIORef emptyCache
+    configCache <- newIORef ("", Nothing)
     return SystemInterface {
-        siReadFile = get cache inputs
+        siReadFile = get cache inputs,
+        siFindSource = findSourceFile inputs (sourcePaths options),
+        siGetConfig = getConfig configCache
     }
   where
     emptyCache :: Map.Map FilePath String
     emptyCache = Map.empty
+
     get cache inputs file = do
         map <- readIORef cache
         case Map.lookup file map of
@@ -344,7 +418,6 @@ ioInterface options files = do
             return $ Right contents
             ) `catch` handler
           else return $ Left (file ++ " was not specified as input (see shellcheck -x).")
-
       where
         handler :: IOException -> IO (Either ErrorMessage String)
         handler ex = return . Left $ show ex
@@ -362,6 +435,82 @@ ioInterface options files = do
         fallback :: FilePath -> IOException -> IO FilePath
         fallback path _ = return path
 
+    -- Returns the name and contents of .shellcheckrc for the given file
+    getConfig cache filename = do
+        path <- normalize filename
+        let dir = takeDirectory path
+        (previousPath, result) <- readIORef cache
+        if dir == previousPath
+          then return result
+          else do
+            paths <- getConfigPaths dir
+            result <- findConfig paths
+            writeIORef cache (dir, result)
+            return result
+
+    findConfig paths =
+        case paths of
+            (file:rest) -> do
+                contents <- readConfig file
+                if isJust contents
+                  then return contents
+                  else findConfig rest
+            [] -> return Nothing
+
+    -- Get a list of candidate filenames. This includes .shellcheckrc
+    -- in all parent directories, plus the user's home dir and xdg dir.
+    -- The dot is optional for Windows and Snap users.
+    getConfigPaths dir = do
+        let next = takeDirectory dir
+        rest <- if next /= dir
+                then getConfigPaths next
+                else defaultPaths `catch`
+                        ((const $ return []) :: IOException -> IO [FilePath])
+        return $ (dir </> ".shellcheckrc") : (dir </> "shellcheckrc") : rest
+
+    defaultPaths = do
+        home <- getAppUserDataDirectory "shellcheckrc"
+        xdg <- getXdgDirectory XdgConfig "shellcheckrc"
+        return [home, xdg]
+
+    readConfig file = do
+        exists <- doesFileExist file
+        if exists
+          then do
+            (contents, _) <- inputFile file `catch` handler file
+            return $ Just (file, contents)
+          else
+            return Nothing
+      where
+        handler :: FilePath -> IOException -> IO (String, Bool)
+        handler file err = do
+            putStrLn $ file ++ ": " ++ show err
+            return ("", True)
+
+    andM a b arg = do
+        first <- a arg
+        if not first then return False else b arg
+
+    findSourceFile inputs sourcePathFlag currentScript sourcePathAnnotation original =
+        if isAbsolute original
+        then
+            let (_, relative) = splitDrive original
+            in find relative original
+        else
+            find original original
+      where
+        find filename deflt = do
+            sources <- filterM ((allowable inputs) `andM` doesFileExist) $
+                        (adjustPath filename):(map (</> filename) $ map adjustPath $ sourcePathFlag ++ sourcePathAnnotation)
+            case sources of
+                [] -> return deflt
+                (first:_) -> return first
+        scriptdir = dropFileName currentScript
+        adjustPath str =
+            case (splitDirectories str) of
+                ("SCRIPTDIR":rest) -> joinPath (scriptdir:rest)
+                _ -> str
+
 inputFile file = do
     (handle, shouldCache) <-
             if file == "-"
@@ -418,3 +567,14 @@ printVersion = do
     putStrLn $ "version: " ++ shellcheckVersion
     putStrLn   "license: GNU General Public License, version 3"
     putStrLn   "website: https://www.shellcheck.net"
+
+printOptional = do
+    mapM f list
+  where
+    list = sortOn cdName ShellCheck.Analyzer.optionalChecks
+    f item = do
+        putStrLn $ "name:    " ++ cdName item
+        putStrLn $ "desc:    " ++ cdDescription item
+        putStrLn $ "example: " ++ cdPositive item
+        putStrLn $ "fix:     " ++ cdNegative item
+        putStrLn ""

snap/snapcraft.yaml

@@ -23,7 +23,8 @@ description: |
       # snap connect shellcheck:removable-media
   
 version: git
-grade: devel
+base: core18
+grade: stable
 confinement: strict
 
 apps:
@@ -34,13 +35,20 @@ apps:
 parts:
   shellcheck:
     plugin: dump
-    source: ./
+    source: .
     build-packages:
       - cabal-install
-    build: |
+      - squid
+    override-build: |
+      # See comments in .snapsquid.conf
+      [ "$http_proxy" ] && {
+        squid3 -f .snapsquid.conf
+        export http_proxy="http://localhost:8888"
+        sleep 3
+      }
       cabal sandbox init
-      cabal update
+      cabal update || cat /var/log/squid/*
       cabal install -j
-    install: |
+
       install -d $SNAPCRAFT_PART_INSTALL/usr/bin
       install .cabal-sandbox/bin/shellcheck $SNAPCRAFT_PART_INSTALL/usr/bin

src/ShellCheck/AST.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -76,7 +76,7 @@ data Token =
     | T_DSEMI Id
     | T_Do Id
     | T_DollarArithmetic Id Token
-    | T_DollarBraced Id Token
+    | T_DollarBraced Id Bool Token
     | T_DollarBracket Id Token
     | T_DollarDoubleQuoted Id [Token]
     | T_DollarExpansion Id [Token]
@@ -121,7 +121,7 @@ data Token =
     | T_Rbrace Id
     | T_Redirecting Id [Token] Token
     | T_Rparen Id
-    | T_Script Id String [Token]
+    | T_Script Id Token [Token] -- Shebang T_Literal, followed by script.
     | T_Select Id
     | T_SelectIn Id String [Token] [Token]
     | T_Semi Id
@@ -139,12 +139,15 @@ data Token =
     | T_CoProcBody Id Token
     | T_Include Id Token
     | T_SourceCommand Id Token Token
+    | T_BatsTest Id Token Token
     deriving (Show)
 
 data Annotation =
     DisableComment Integer
+    | EnableComment String
     | SourceOverride String
     | ShellOverride String
+    | SourcePath String
     deriving (Show, Eq)
 data ConditionType = DoubleBracket | SingleBracket deriving (Show, Eq)
 
@@ -250,7 +253,7 @@ analyze f g i =
     delve (T_Function id a b name body) = d1 body $ T_Function id a b name
     delve (T_Condition id typ token) = d1 token $ T_Condition id typ
     delve (T_Extglob id str l) = dl l $ T_Extglob id str
-    delve (T_DollarBraced id op) = d1 op $ T_DollarBraced id
+    delve (T_DollarBraced id braced op) = d1 op $ T_DollarBraced id braced
     delve (T_HereDoc id d q str l) = dl l $ T_HereDoc id d q str
 
     delve (TC_And id typ str t1 t2) = d2 t1 t2 $ TC_And id typ str
@@ -276,6 +279,7 @@ analyze f g i =
     delve (T_CoProcBody id t) = d1 t $ T_CoProcBody id
     delve (T_Include id script) = d1 script $ T_Include id
     delve (T_SourceCommand id includer t_include) = d2 includer t_include $ T_SourceCommand id
+    delve (T_BatsTest id name t) = d2 name t $ T_BatsTest id
     delve t = return t
 
 getId :: Token -> Id
@@ -319,7 +323,7 @@ getId t = case t of
         T_NormalWord id _  -> id
         T_DoubleQuoted id _  -> id
         T_DollarExpansion id _  -> id
-        T_DollarBraced id _  -> id
+        T_DollarBraced id _ _ -> id
         T_DollarArithmetic id _  -> id
         T_BraceExpansion id _  -> id
         T_ParamSubSpecialChar id _ -> id
@@ -380,6 +384,7 @@ getId t = case t of
         T_UnparsedIndex id _ _ -> id
         TC_Empty id _ -> id
         TA_Variable id _ _ -> id
+        T_BatsTest id _ _ -> id
 
 blank :: Monad m => Token -> m ()
 blank = const $ return ()

src/ShellCheck/ASTLib.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -81,7 +81,7 @@ oversimplify token =
         (T_NormalWord _ l) -> [concat (concatMap oversimplify l)]
         (T_DoubleQuoted _ l) -> [concat (concatMap oversimplify l)]
         (T_SingleQuoted _ s) -> [s]
-        (T_DollarBraced _ _) -> ["${VAR}"]
+        (T_DollarBraced _ _ _) -> ["${VAR}"]
         (T_DollarArithmetic _ _) -> ["${VAR}"]
         (T_DollarExpansion _ _) -> ["${VAR}"]
         (T_Backticked _ _) -> ["${VAR}"]
@@ -133,11 +133,11 @@ isUnquotedFlag token = fromMaybe False $ do
     return $ "-" `isPrefixOf` str
 
 -- Given a T_DollarBraced, return a simplified version of the string contents.
-bracedString (T_DollarBraced _ l) = concat $ oversimplify l
+bracedString (T_DollarBraced _ _ l) = concat $ oversimplify l
 bracedString _ = error "Internal shellcheck error, please report! (bracedString on non-variable)"
 
 -- Is this an expansion of multiple items of an array?
-isArrayExpansion t@(T_DollarBraced _ _) =
+isArrayExpansion t@(T_DollarBraced _ _ _) =
     let string = bracedString t in
         "@" `isPrefixOf` string ||
             not ("#" `isPrefixOf` string) && "[@]" `isInfixOf` string
@@ -146,7 +146,7 @@ isArrayExpansion _ = False
 -- Is it possible that this arg becomes multiple args?
 mayBecomeMultipleArgs t = willBecomeMultipleArgs t || f t
   where
-    f t@(T_DollarBraced _ _) =
+    f t@(T_DollarBraced _ _ _) =
         let string = bracedString t in
             "!" `isPrefixOf` string
     f (T_DoubleQuoted _ parts) = any f parts
@@ -351,6 +351,14 @@ isOnlyRedirection t =
 
 isFunction t = case t of T_Function {} -> True; _ -> False
 
+-- Bats tests are functions for the purpose of 'local' and such
+isFunctionLike t =
+    case t of
+        T_Function {} -> True
+        T_BatsTest {} -> True
+        _ -> False
+
+
 isBraceExpansion t = case t of T_BraceExpansion {} -> True; _ -> False
 
 -- Get the lists of commands from tokens that contain them, such as
@@ -485,8 +493,21 @@ wordsCanBeEqual x y = fromMaybe True $
 -- Is this an expansion that can be quoted,
 -- e.g. $(foo) `foo` $foo (but not {foo,})?
 isQuoteableExpansion t = case t of
+    T_DollarBraced {} -> True
+    _ -> isCommandSubstitution t
+
+isCommandSubstitution t = case t of
     T_DollarExpansion {} -> True
     T_DollarBraceCommandExpansion {} -> True
     T_Backticked {} -> True
-    T_DollarBraced {} -> True
     _ -> False
+
+
+-- Is this a T_Annotation that ignores a specific code?
+isAnnotationIgnoringCode code t =
+    case t of
+        T_Annotation _ anns _ -> any hasNum anns
+        _ -> False
+  where
+    hasNum (DisableComment ts) = code == ts
+    hasNum _                   = False

src/ShellCheck/Analyzer.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -17,7 +17,7 @@
     You should have received a copy of the GNU General Public License
     along with this program.  If not, see <https://www.gnu.org/licenses/>.
 -}
-module ShellCheck.Analyzer (analyzeScript) where
+module ShellCheck.Analyzer (analyzeScript, ShellCheck.Analyzer.optionalChecks) where
 
 import ShellCheck.Analytics
 import ShellCheck.AnalyzerLib
@@ -25,6 +25,7 @@ import ShellCheck.Interface
 import Data.List
 import Data.Monoid
 import qualified ShellCheck.Checks.Commands
+import qualified ShellCheck.Checks.Custom
 import qualified ShellCheck.Checks.ShellSupport
 
 
@@ -41,5 +42,10 @@ analyzeScript spec = newAnalysisResult {
 
 checkers params = mconcat $ map ($ params) [
     ShellCheck.Checks.Commands.checker,
+    ShellCheck.Checks.Custom.checker,
     ShellCheck.Checks.ShellSupport.checker
     ]
+
+optionalChecks = mconcat $ [
+    ShellCheck.Analytics.optionalChecks
+    ]

src/ShellCheck/AnalyzerLib.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -77,15 +77,23 @@ composeAnalyzers :: (a -> Analysis) -> (a -> Analysis) -> a -> Analysis
 composeAnalyzers f g x = f x >> g x
 
 data Parameters = Parameters {
-    hasLastpipe        :: Bool,           -- Whether this script has the 'lastpipe' option set/default.
-    hasSetE            :: Bool,           -- Whether this script has 'set -e' anywhere.
-    variableFlow       :: [StackData],   -- A linear (bad) analysis of data flow
-    parentMap          :: Map.Map Id Token, -- A map from Id to parent Token
-    shellType          :: Shell,            -- The shell type, such as Bash or Ksh
-    shellTypeSpecified :: Bool,    -- True if shell type was forced via flags
-    rootNode           :: Token,              -- The root node of the AST
-    tokenPositions     :: Map.Map Id (Position, Position) -- map from token id to start and end position
-    }
+    -- Whether this script has the 'lastpipe' option set/default.
+    hasLastpipe        :: Bool,
+    -- Whether this script has 'set -e' anywhere.
+    hasSetE            :: Bool,
+    -- A linear (bad) analysis of data flow
+    variableFlow       :: [StackData],
+    -- A map from Id to parent Token
+    parentMap          :: Map.Map Id Token,
+    -- The shell type, such as Bash or Ksh
+    shellType          :: Shell,
+    -- True if shell type was forced via flags
+    shellTypeSpecified :: Bool,
+    -- The root node of the AST
+    rootNode           :: Token,
+    -- map from token id to start and end position
+    tokenPositions     :: Map.Map Id (Position, Position)
+    } deriving (Show)
 
 -- TODO: Cache results of common AST ops here
 data Cache = Cache {}
@@ -112,11 +120,12 @@ data DataSource =
 
 data VariableState = Dead Token String | Alive deriving (Show)
 
-defaultSpec root = spec {
+defaultSpec pr = spec {
     asShellType = Nothing,
     asCheckSourced = False,
-    asExecutionMode = Executed
-} where spec = newAnalysisSpec root
+    asExecutionMode = Executed,
+    asTokenPositions = prTokenPositions pr
+} where spec = newAnalysisSpec (fromJust $ prRoot pr)
 
 pScript s =
   let
@@ -124,13 +133,14 @@ pScript s =
         psFilename = "script",
         psScript = s
     }
-  in prRoot . runIdentity $ parseScript (mockedSystemInterface []) pSpec
+  in runIdentity $ parseScript (mockedSystemInterface []) pSpec
 
 -- For testing. If parsed, returns whether there are any comments
 producesComments :: Checker -> String -> Maybe Bool
 producesComments c s = do
-        root <- pScript s
-        let spec = defaultSpec root
+        let pr = pScript s
+        prRoot pr
+        let spec = defaultSpec pr
         let params = makeParameters spec
         return . not . null $ runChecker params c
 
@@ -153,11 +163,14 @@ err   id code str = addComment $ makeComment ErrorC id code str
 info  id code str = addComment $ makeComment InfoC id code str
 style id code str = addComment $ makeComment StyleC id code str
 
-warnWithFix id code str fix = addComment $
-    let comment = makeComment WarningC id code str in
-    comment {
-        tcFix = Just fix
-    }
+warnWithFix :: MonadWriter [TokenComment] m => Id -> Code -> String -> Fix -> m ()
+warnWithFix  = addCommentWithFix WarningC
+styleWithFix :: MonadWriter [TokenComment] m => Id -> Code -> String -> Fix -> m ()
+styleWithFix = addCommentWithFix StyleC
+
+addCommentWithFix :: MonadWriter [TokenComment] m => Severity -> Id -> Code -> String -> Fix -> m ()
+addCommentWithFix severity id code str fix =
+    addComment $ makeCommentWithFix severity id code str fix
 
 makeCommentWithFix :: Severity -> Id -> Code -> String -> Fix -> TokenComment
 makeCommentWithFix severity id code str fix =
@@ -170,7 +183,7 @@ makeCommentWithFix severity id code str fix =
 makeParameters spec =
     let params = Parameters {
         rootNode = root,
-        shellType = fromMaybe (determineShell root) $ asShellType spec,
+        shellType = fromMaybe (determineShell (asFallbackShell spec) root) $ asShellType spec,
         hasSetE = containsSetE root,
         hasLastpipe =
             case shellType params of
@@ -179,7 +192,7 @@ makeParameters spec =
                 Sh   -> False
                 Ksh  -> True,
 
-        shellTypeSpecified = isJust $ asShellType spec,
+        shellTypeSpecified = isJust (asShellType spec) || isJust (asFallbackShell spec),
         parentMap = getParentTree root,
         variableFlow = getVariableFlow params root,
         tokenPositions = asTokenPositions spec
@@ -193,7 +206,7 @@ containsSetE root = isNothing $ doAnalysis (guard . not . isSetE) root
   where
     isSetE t =
         case t of
-            T_Script _ str _ -> str `matches` re
+            T_Script _ (T_Literal _ str) _ -> str `matches` re
             T_SimpleCommand {}  ->
                 t `isUnqualifiedCommand` "set" &&
                     ("errexit" `elem` oversimplify t ||
@@ -214,19 +227,21 @@ containsLastpipe root =
                 _ -> False
 
 
-prop_determineShell0 = determineShell (fromJust $ pScript "#!/bin/sh") == Sh
-prop_determineShell1 = determineShell (fromJust $ pScript "#!/usr/bin/env ksh") == Ksh
-prop_determineShell2 = determineShell (fromJust $ pScript "") == Bash
-prop_determineShell3 = determineShell (fromJust $ pScript "#!/bin/sh -e") == Sh
-prop_determineShell4 = determineShell (fromJust $ pScript
-    "#!/bin/ksh\n#shellcheck shell=sh\nfoo") == Sh
-prop_determineShell5 = determineShell (fromJust $ pScript
-    "#shellcheck shell=sh\nfoo") == Sh
-prop_determineShell6 = determineShell (fromJust $ pScript "#! /bin/sh") == Sh
-prop_determineShell7 = determineShell (fromJust $ pScript "#! /bin/ash") == Dash
-determineShell t = fromMaybe Bash $ do
+prop_determineShell0 = determineShellTest "#!/bin/sh" == Sh
+prop_determineShell1 = determineShellTest "#!/usr/bin/env ksh" == Ksh
+prop_determineShell2 = determineShellTest "" == Bash
+prop_determineShell3 = determineShellTest "#!/bin/sh -e" == Sh
+prop_determineShell4 = determineShellTest "#!/bin/ksh\n#shellcheck shell=sh\nfoo" == Sh
+prop_determineShell5 = determineShellTest "#shellcheck shell=sh\nfoo" == Sh
+prop_determineShell6 = determineShellTest "#! /bin/sh" == Sh
+prop_determineShell7 = determineShellTest "#! /bin/ash" == Dash
+prop_determineShell8 = determineShellTest' (Just Ksh) "#!/bin/sh" == Sh
+
+determineShellTest = determineShellTest' Nothing
+determineShellTest' fallbackShell = determineShell fallbackShell . fromJust . prRoot . pScript
+determineShell fallbackShell t = fromMaybe Bash $ do
     shellString <- foldl mplus Nothing $ getCandidates t
-    shellForExecutable shellString
+    shellForExecutable shellString `mplus` fallbackShell
   where
     forAnnotation t =
         case t of
@@ -237,7 +252,7 @@ determineShell t = fromMaybe Bash $ do
     getCandidates (T_Annotation _ annotations s) =
         map forAnnotation annotations ++
            [Just $ fromShebang s]
-    fromShebang (T_Script _ s t) = executableFromShebang s
+    fromShebang (T_Script _ (T_Literal _ s) _) = executableFromShebang s
 
 -- Given a string like "/bin/bash" or "/usr/bin/env dash",
 -- return the shell basename like "bash" or "dash"
@@ -375,10 +390,6 @@ isParentOf tree parent child =
 
 parents params = getPath (parentMap params)
 
-pathTo t = do
-    parents <- reader parentMap
-    return $ getPath parents t
-
 -- Find the first match in a list where the predicate is Just True.
 -- Stops if it's Just False and ignores Nothing.
 findFirst :: (a -> Maybe Bool) -> [a] -> Maybe a
@@ -422,6 +433,7 @@ getVariableFlow params t =
 
     assignFirst T_ForIn {}    = True
     assignFirst T_SelectIn {} = True
+    assignFirst (T_BatsTest {}) = True
     assignFirst _             = False
 
     setRead t =
@@ -439,6 +451,7 @@ leadType params t =
         T_Backticked _ _  -> SubshellScope "`..` expansion"
         T_Backgrounded _ _  -> SubshellScope "backgrounding &"
         T_Subshell _ _  -> SubshellScope "(..) group"
+        T_BatsTest {} -> SubshellScope "@bats test"
         T_CoProcBody _ _  -> SubshellScope "coproc"
         T_Redirecting {}  ->
             if fromMaybe False causesSubshell
@@ -479,6 +492,12 @@ getModifiedVariables t =
             guard $ op `elem` ["=", "*=", "/=", "%=", "+=", "-=", "<<=", ">>=", "&=", "^=", "|="]
             return (t, t, name, DataString $ SourceFrom [rhs])
 
+        T_BatsTest {} -> [
+            (t, t, "lines", DataArray SourceExternal),
+            (t, t, "status", DataString SourceInteger),
+            (t, t, "output", DataString SourceExternal)
+            ]
+
         -- Count [[ -v foo ]] as an "assignment".
         -- This is to prevent [ -v foo ] being unassigned or unused.
         TC_Unary id _ "-v" token -> maybeToList $ do
@@ -491,7 +510,7 @@ getModifiedVariables t =
             guard . not . null $ str
             return (t, token, str, DataString SourceChecked)
 
-        T_DollarBraced _ l -> maybeToList $ do
+        T_DollarBraced _ _ l -> maybeToList $ do
             let string = bracedString t
             let modifier = getBracedModifier string
             guard $ ":=" `isPrefixOf` modifier
@@ -527,10 +546,6 @@ getReferencedVariableCommand base@(T_SimpleCommand _ _ (T_NormalWord _ (T_Litera
                     (not $ any (`elem` flags) ["f", "F"])
             then concatMap getReference rest
             else []
-        "readonly" ->
-            if any (`elem` flags) ["f", "p"]
-            then []
-            else concatMap getReference rest
         "trap" ->
             case rest of
                 head:_ -> map (\x -> (head, head, x)) $ getVariablesFromLiteralToken head
@@ -587,6 +602,11 @@ getModifiedVariableCommand base@(T_SimpleCommand _ _ (T_NormalWord _ (T_Literal
         "mapfile" -> maybeToList $ getMapfileArray base rest
         "readarray" -> maybeToList $ getMapfileArray base rest
 
+        "DEFINE_boolean" -> maybeToList $ getFlagVariable rest
+        "DEFINE_float" -> maybeToList $ getFlagVariable rest
+        "DEFINE_integer" -> maybeToList $ getFlagVariable rest
+        "DEFINE_string" -> maybeToList $ getFlagVariable rest
+
         _ -> []
   where
     flags = map snd $ getAllFlags base
@@ -638,7 +658,11 @@ getModifiedVariableCommand base@(T_SimpleCommand _ _ (T_NormalWord _ (T_Literal
 
     getPrintfVariable list = f $ map (\x -> (x, getLiteralString x)) list
       where
-        f ((_, Just "-v") : (t, Just var) : _) = return (base, t, var, DataString $ SourceFrom list)
+        f ((_, Just "-v") : (t, Just var) : _) = return (base, t, varName, varType $ SourceFrom list)
+            where
+                (varName, varType) = case elemIndex '[' var of
+                    Just i -> (take i var, DataArray)
+                    Nothing -> (var, DataString)
         f (_:rest) = f rest
         f [] = fail "not found"
 
@@ -652,9 +676,22 @@ getModifiedVariableCommand base@(T_SimpleCommand _ _ (T_NormalWord _ (T_Literal
         return (base, lastArg, name, DataArray SourceExternal)
 
     -- get all the array variables used in read, e.g. read -a arr
-    getReadArrayVariables args = do
+    getReadArrayVariables args =
         map (getLiteralArray . snd)
-            (filter (\(x,_) -> getLiteralString x == Just "-a") (zip (args) (tail args)))
+            (filter (isArrayFlag . fst) (zip args (tail args)))
+
+    isArrayFlag x = fromMaybe False $ do
+        str <- getLiteralString x
+        return $ case str of
+                    '-':'-':_ -> False
+                    '-':str -> 'a' `elem` str
+                    _ -> False
+
+    -- get the FLAGS_ variable created by a shflags DEFINE_ call
+    getFlagVariable (n:v:_) = do
+        name <- getLiteralString n
+        return (base, n, "FLAGS_" ++ name, DataString $ SourceExternal)
+    getFlagVariable _ = Nothing
 
 getModifiedVariableCommand _ = []
 
@@ -679,7 +716,7 @@ getOffsetReferences mods = fromMaybe [] $ do
 
 getReferencedVariables parents t =
     case t of
-        T_DollarBraced id l -> let str = bracedString t in
+        T_DollarBraced id _ l -> let str = bracedString t in
             (t, t, getBracedReference str) :
                 map (\x -> (l, l, x)) (
                     getIndexReferences str
@@ -698,6 +735,12 @@ getReferencedVariables parents t =
             then concatMap (getIfReference t) [lhs, rhs]
             else []
 
+        T_BatsTest {} -> [ -- pretend @test references vars to avoid warnings
+            (t, t, "lines"),
+            (t, t, "status"),
+            (t, t, "output")
+            ]
+
         t@(T_FdRedirect _ ('{':var) op) -> -- {foo}>&- references and closes foo
             [(t, t, takeWhile (/= '}') var) | isClosingFileOp op]
         x -> getReferencedVariableCommand x
@@ -748,7 +791,7 @@ isCommandMatch token matcher = fromMaybe False $
 -- False: .*foo.*
 isConfusedGlobRegex :: String -> Bool
 isConfusedGlobRegex ('*':_) = True
-isConfusedGlobRegex [x,'*'] | x /= '\\' = True
+isConfusedGlobRegex [x,'*'] | x `notElem` "\\." = True
 isConfusedGlobRegex _       = False
 
 isVariableStartChar x = x == '_' || isAsciiLower x || isAsciiUpper x
@@ -858,18 +901,17 @@ filterByAnnotation asSpec params =
     shouldIgnore note =
         any (shouldIgnoreFor (getCode note)) $
             getPath parents (T_Bang $ tcId note)
-    shouldIgnoreFor num (T_Annotation _ anns _) =
-        any hasNum anns
-      where
-        hasNum (DisableComment ts) = num == ts
-        hasNum _                   = False
     shouldIgnoreFor _ T_Include {} = not $ asCheckSourced asSpec
-    shouldIgnoreFor _ _ = False
+    shouldIgnoreFor code t = isAnnotationIgnoringCode code t
     parents = parentMap params
     getCode = cCode . tcComment
 
+shouldIgnoreCode params code t =
+    any (isAnnotationIgnoringCode code) $
+        getPath (parentMap params) t
+
 -- Is this a ${#anything}, to get string length or array count?
-isCountingReference (T_DollarBraced id token) =
+isCountingReference (T_DollarBraced id _ token) =
     case concat $ oversimplify token of
         '#':_ -> True
         _     -> False
@@ -878,7 +920,7 @@ isCountingReference _ = False
 -- FIXME: doesn't handle ${a:+$var} vs ${a:+"$var"}
 isQuotedAlternativeReference t =
     case t of
-        T_DollarBraced _ _ ->
+        T_DollarBraced _ _ _ ->
             getBracedModifier (bracedString t) `matches` re
         _ -> False
   where
@@ -917,5 +959,16 @@ getOpts flagTokenizer string cmd = process flags
                 more <- process rest2
                 return $ (flag1, token1) : more
 
+supportsArrays shell = shell == Bash || shell == Ksh
+
+-- Returns true if the shell is Bash or Ksh (sorry for the name, Ksh)
+isBashLike :: Parameters -> Bool
+isBashLike params =
+    case shellType params of
+        Bash -> True
+        Ksh -> True
+        Dash -> False
+        Sh -> False
+
 return []
 runTests =  $( [| $(forAllProperties) (quickCheckWithResult (stdArgs { maxSuccess = 1 }) ) |])

src/ShellCheck/Checker.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -48,6 +48,17 @@ tokenToPosition startMap t = fromMaybe fail $ do
   where
     fail = error "Internal shellcheck error: id doesn't exist. Please report!"
 
+shellFromFilename filename = foldl mplus Nothing candidates
+  where
+    shellExtensions = [(".ksh", Ksh)
+                      ,(".bash", Bash)
+                      ,(".bats", Bash)
+                      ,(".dash", Dash)]
+                      -- The `.sh` is too generic to determine the shell:
+                      -- We fallback to Bash in this case and emit SC2148 if there is no shebang
+    candidates =
+        map (\(ext,sh) -> if ext `isSuffixOf` filename then Just sh else Nothing) shellExtensions
+
 checkScript :: Monad m => SystemInterface m -> CheckSpec -> m CheckResult
 checkScript sys spec = do
     results <- checkScript (csScript spec)
@@ -61,6 +72,7 @@ checkScript sys spec = do
             psFilename = csFilename spec,
             psScript = contents,
             psCheckSourced = csCheckSourced spec,
+            psIgnoreRC = csIgnoreRC spec,
             psShellTypeOverride = csShellTypeOverride spec
         }
         let parseMessages = prComments result
@@ -69,9 +81,11 @@ checkScript sys spec = do
                 as {
                     asScript = root,
                     asShellType = csShellTypeOverride spec,
+                    asFallbackShell = shellFromFilename $ csFilename spec,
                     asCheckSourced = csCheckSourced spec,
                     asExecutionMode = Executed,
-                    asTokenPositions = tokenPositions
+                    asTokenPositions = tokenPositions,
+                    asOptionalChecks = csOptionalChecks spec
                 } where as = newAnalysisSpec root
         let analysisMessages =
                 fromMaybe [] $
@@ -82,11 +96,13 @@ checkScript sys spec = do
             (parseMessages ++ map translator analysisMessages)
 
     shouldInclude pc =
-        let code     = cCode (pcComment pc)
+            severity <= csMinSeverity spec &&
+            case csIncludedWarnings spec of
+                Nothing -> code `notElem` csExcludedWarnings spec
+                Just includedWarnings -> code `elem` includedWarnings
+        where
+            code     = cCode (pcComment pc)
             severity = cSeverity (pcComment pc)
-        in
-            code `notElem` csExcludedWarnings spec &&
-            severity <= csMinSeverity spec
 
     sortMessages = sortBy (comparing order)
     order pc =
@@ -125,6 +141,21 @@ checkRecursive includes src =
         csCheckSourced = True
     }
 
+checkOptionIncludes includes src =
+    checkWithSpec [] emptyCheckSpec {
+        csScript = src,
+        csIncludedWarnings = includes,
+        csCheckSourced = True
+    }
+
+checkWithRc rc = getErrors
+    (mockRcFile rc $ mockedSystemInterface [])
+
+checkWithIncludesAndSourcePath includes mapper = getErrors
+    (mockedSystemInterface includes) {
+        siFindSource = mapper
+    }
+
 prop_findsParseIssue = check "echo \"$12\"" == [1037]
 
 prop_commentDisablesParseIssue1 =
@@ -179,9 +210,13 @@ prop_failsWhenNotSourcing =
 prop_worksWhenSourcing =
     null $ checkWithIncludes [("lib", "bar=1")] "source lib; echo \"$bar\""
 
+prop_worksWhenSourcingWithDashDash =
+    null $ checkWithIncludes [("lib", "bar=1")] "source -- lib; echo \"$bar\""
+
 prop_worksWhenDotting =
     null $ checkWithIncludes [("lib", "bar=1")] ". lib; echo \"$bar\""
 
+-- FIXME: This should really be giving [1093], "recursively sourced"
 prop_noInfiniteSourcing =
     [] == checkWithIncludes  [("lib", "source lib")] "source lib"
 
@@ -203,6 +238,12 @@ prop_recursiveAnalysis =
 prop_recursiveParsing =
     [1037] == checkRecursive [("lib", "echo \"$10\"")] "source lib"
 
+prop_nonRecursiveAnalysis =
+    [] == checkWithIncludes [("lib", "echo $1")] "source lib"
+
+prop_nonRecursiveParsing =
+    [] == checkWithIncludes [("lib", "echo \"$10\"")] "source lib"
+
 prop_sourceDirectiveDoesntFollowFile =
     null $ checkWithIncludes
                 [("foo", "source bar"), ("bar", "baz=3")]
@@ -231,5 +272,123 @@ prop_filewideAnnotation8 = null $
 prop_sourcePartOfOriginalScript = -- #1181: -x disabled posix warning for 'source'
     2039 `elem` checkWithIncludes [("./saywhat.sh", "echo foo")] "#!/bin/sh\nsource ./saywhat.sh"
 
+prop_spinBug1413 = null $ check "fun() {\n# shellcheck disable=SC2188\n> /dev/null\n}\n"
+
+prop_deducesTypeFromExtension = null result
+  where
+    result = checkWithSpec [] emptyCheckSpec {
+        csFilename = "file.ksh",
+        csScript = "(( 3.14 ))"
+    }
+
+prop_deducesTypeFromExtension2 = result == [2079]
+  where
+    result = checkWithSpec [] emptyCheckSpec {
+        csFilename = "file.bash",
+        csScript = "(( 3.14 ))"
+    }
+
+prop_shExtensionDoesntMatter = result == [2148]
+  where
+    result = checkWithSpec [] emptyCheckSpec {
+        csFilename = "file.sh",
+        csScript = "echo 'hello world'"
+    }
+
+prop_sourcedFileUsesOriginalShellExtension = result == [2079]
+  where
+    result = checkWithSpec [("file.ksh", "(( 3.14 ))")] emptyCheckSpec {
+        csFilename = "file.bash",
+        csScript = "source file.ksh",
+        csCheckSourced = True
+    }
+
+prop_canEnableOptionalsWithSpec = result == [2244]
+  where
+    result = checkWithSpec [] emptyCheckSpec {
+        csFilename = "file.sh",
+        csScript = "#!/bin/sh\n[ \"$1\" ]",
+        csOptionalChecks = ["avoid-nullary-conditions"]
+    }
+
+prop_optionIncludes1 =
+    -- expect 2086, but not included, so nothing reported
+    null $ checkOptionIncludes (Just [2080]) "#!/bin/sh\n var='a b'\n echo $var"
+
+prop_optionIncludes2 =
+    -- expect 2086, included, so it is reported
+    [2086] == checkOptionIncludes (Just [2086]) "#!/bin/sh\n var='a b'\n echo $var"
+
+prop_optionIncludes3 =
+    -- expect 2086, no inclusions provided, so it is reported
+    [2086] == checkOptionIncludes Nothing "#!/bin/sh\n var='a b'\n echo $var"
+
+prop_optionIncludes4 =
+    -- expect 2086 & 2154, only 2154 included, so only that's reported
+    [2154] == checkOptionIncludes (Just [2154]) "#!/bin/sh\n var='a b'\n echo $var\n echo $bar"
+
+
+prop_readsRcFile = result == []
+  where
+    result = checkWithRc "disable=2086" emptyCheckSpec {
+        csScript = "#!/bin/sh\necho $1",
+        csIgnoreRC = False
+    }
+
+prop_canUseNoRC = result == [2086]
+  where
+    result = checkWithRc "disable=2086" emptyCheckSpec {
+        csScript = "#!/bin/sh\necho $1",
+        csIgnoreRC = True
+    }
+
+prop_NoRCWontLookAtFile = result == [2086]
+  where
+    result = checkWithRc (error "Fail") emptyCheckSpec {
+        csScript = "#!/bin/sh\necho $1",
+        csIgnoreRC = True
+    }
+
+prop_brokenRcGetsWarning = result == [1134, 2086]
+  where
+    result = checkWithRc "rofl" emptyCheckSpec {
+        csScript = "#!/bin/sh\necho $1",
+        csIgnoreRC = False
+    }
+
+prop_canEnableOptionalsWithRc = result == [2244]
+  where
+    result = checkWithRc "enable=avoid-nullary-conditions" emptyCheckSpec {
+        csScript = "#!/bin/sh\n[ \"$1\" ]"
+    }
+
+prop_sourcePathRedirectsName = result == [2086]
+  where
+    f "dir/myscript" _ "lib" = return "foo/lib"
+    result = checkWithIncludesAndSourcePath [("foo/lib", "echo $1")] f emptyCheckSpec {
+        csScript = "#!/bin/bash\nsource lib",
+        csFilename = "dir/myscript",
+        csCheckSourced = True
+    }
+
+prop_sourcePathAddsAnnotation = result == [2086]
+  where
+    f "dir/myscript" ["mypath"] "lib" = return "foo/lib"
+    result = checkWithIncludesAndSourcePath [("foo/lib", "echo $1")] f emptyCheckSpec {
+        csScript = "#!/bin/bash\n# shellcheck source-path=mypath\nsource lib",
+        csFilename = "dir/myscript",
+        csCheckSourced = True
+    }
+
+prop_sourcePathRedirectsDirective = result == [2086]
+  where
+    f "dir/myscript" _ "lib" = return "foo/lib"
+    f _ _ _ = return "/dev/null"
+    result = checkWithIncludesAndSourcePath [("foo/lib", "echo $1")] f emptyCheckSpec {
+        csScript = "#!/bin/bash\n# shellcheck source=lib\nsource kittens",
+        csFilename = "dir/myscript",
+        csCheckSourced = True
+    }
+
 return []
 runTests = $quickCheckAll

src/ShellCheck/Checks/Commands.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -61,6 +61,7 @@ commandChecks = [
     ,checkGrepRe
     ,checkTrapQuotes
     ,checkReturn
+    ,checkExit
     ,checkFindExecWithSingleArgument
     ,checkUnusedEchoEscapes
     ,checkInjectableFindSh
@@ -92,6 +93,8 @@ commandChecks = [
     ,checkWhich
     ,checkSudoRedirect
     ,checkSudoArgs
+    ,checkSourceArgs
+    ,checkChmodDashr
     ]
 
 buildCommandMap :: [CommandCheck] -> Map.Map CommandName (Token -> Analysis)
@@ -206,6 +209,14 @@ prop_checkGrepRe12= verifyNot checkGrepRe "grep -F 'Foo*' file"
 prop_checkGrepRe13= verifyNot checkGrepRe "grep -- -foo bar*"
 prop_checkGrepRe14= verifyNot checkGrepRe "grep -e -foo bar*"
 prop_checkGrepRe15= verifyNot checkGrepRe "grep --regex -foo bar*"
+prop_checkGrepRe16= verifyNot checkGrepRe "grep --include 'Foo*' file"
+prop_checkGrepRe17= verifyNot checkGrepRe "grep --exclude 'Foo*' file"
+prop_checkGrepRe18= verifyNot checkGrepRe "grep --exclude-dir 'Foo*' file"
+prop_checkGrepRe19= verify checkGrepRe "grep -- 'Foo*' file"
+prop_checkGrepRe20= verifyNot checkGrepRe "grep --fixed-strings 'Foo*' file"
+prop_checkGrepRe21= verifyNot checkGrepRe "grep -o 'x*' file"
+prop_checkGrepRe22= verifyNot checkGrepRe "grep --only-matching 'x*' file"
+prop_checkGrepRe23= verifyNot checkGrepRe "grep '.*' file"
 
 checkGrepRe = CommandCheck (Basename "grep") check where
     check cmd = f cmd (arguments cmd)
@@ -228,7 +239,7 @@ checkGrepRe = CommandCheck (Basename "grep") check where
         when (isGlob re) $
             warn (getId re) 2062 "Quote the grep pattern so the shell won't interpret it."
 
-        unless (cmd `hasFlag` "F") $ do
+        unless (any (`elem` flags) grepGlobFlags) $ do
             let string = concat $ oversimplify re
             if isConfusedGlobRegex string then
                 warn (getId re) 2063 "Grep uses regex, but this looks like a glob."
@@ -236,6 +247,9 @@ checkGrepRe = CommandCheck (Basename "grep") check where
                 char <- getSuspiciousRegexWildcard string
                 return $ info (getId re) 2022 $
                     "Note that unlike globs, " ++ [char] ++ "* here matches '" ++ [char, char, char] ++ "' but not '" ++ wordStartingWith char ++ "'."
+      where
+        flags = map snd $ getAllFlags cmd
+        grepGlobFlags = ["fixed-strings", "F", "include", "exclude", "exclude-dir", "o", "only-matching"]
 
     wordStartingWith c =
         head . filter ([c] `isPrefixOf`) $ candidates
@@ -268,7 +282,7 @@ checkTrapQuotes = CommandCheck (Exactly "trap") (f . arguments) where
     warning id = warn id 2064 "Use single quotes, otherwise this expands now rather than when signalled."
     checkExpansions (T_DollarExpansion id _) = warning id
     checkExpansions (T_Backticked id _) = warning id
-    checkExpansions (T_DollarBraced id _) = warning id
+    checkExpansions (T_DollarBraced id _ _) = warning id
     checkExpansions (T_DollarArithmetic id _) = warning id
     checkExpansions _ = return ()
 
@@ -280,15 +294,28 @@ prop_checkReturn4 = verifyNot checkReturn "return $((a|b))"
 prop_checkReturn5 = verify checkReturn "return -1"
 prop_checkReturn6 = verify checkReturn "return 1000"
 prop_checkReturn7 = verify checkReturn "return 'hello world'"
-checkReturn = CommandCheck (Exactly "return") (f . arguments)
+checkReturn = CommandCheck (Exactly "return") (returnOrExit
+        (\c -> err c 2151 "Only one integer 0-255 can be returned. Use stdout for other data.")
+        (\c -> err c 2152 "Can only return 0-255. Other data should be written to stdout."))
+
+prop_checkExit1 = verifyNot checkExit "exit"
+prop_checkExit2 = verifyNot checkExit "exit 1"
+prop_checkExit3 = verifyNot checkExit "exit $var"
+prop_checkExit4 = verifyNot checkExit "exit $((a|b))"
+prop_checkExit5 = verify checkExit "exit -1"
+prop_checkExit6 = verify checkExit "exit 1000"
+prop_checkExit7 = verify checkExit "exit 'hello world'"
+checkExit = CommandCheck (Exactly "exit") (returnOrExit
+        (\c -> err c 2241 "The exit status can only be one integer 0-255. Use stdout for other data.")
+        (\c -> err c 2242 "Can only exit with status 0-255. Other data should be written to stdout/stderr."))
+
+returnOrExit multi invalid = (f . arguments)
   where
     f (first:second:_) =
-        err (getId second) 2151
-            "Only one integer 0-255 can be returned. Use stdout for other data."
+        multi (getId first)
     f [value] =
         when (isInvalid $ literal value) $
-            err (getId value) 2152
-                "Can only return 0-255. Other data should be written to stdout."
+            invalid (getId value)
     f _ = return ()
 
     isInvalid s = s == "" || any (not . isDigit) s || length s > 5
@@ -462,7 +489,7 @@ prop_checkInteractiveSu4 = verifyNot checkInteractiveSu "su root < script"
 checkInteractiveSu = CommandCheck (Basename "su") f
   where
     f cmd = when (length (arguments cmd) <= 1) $ do
-        path <- pathTo cmd
+        path <- getPathM cmd
         when (all undirected path) $
             info (getId cmd) 2117
                 "To run commands as another user, use su -c or sudo."
@@ -511,52 +538,83 @@ prop_checkPrintfVar15= verifyNot checkPrintfVar "printf '%*s\\n' 1 2"
 prop_checkPrintfVar16= verifyNot checkPrintfVar "printf $'string'"
 prop_checkPrintfVar17= verify checkPrintfVar "printf '%-*s\\n' 1"
 prop_checkPrintfVar18= verifyNot checkPrintfVar "printf '%-*s\\n' 1 2"
+prop_checkPrintfVar19= verifyNot checkPrintfVar "printf '%(%s)T'"
+prop_checkPrintfVar20= verifyNot checkPrintfVar "printf '%d %(%s)T' 42"
+prop_checkPrintfVar21= verify checkPrintfVar "printf '%d %(%s)T'"
 checkPrintfVar = CommandCheck (Exactly "printf") (f . arguments) where
     f (doubledash:rest) | getLiteralString doubledash == Just "--" = f rest
     f (dashv:var:rest) | getLiteralString dashv == Just "-v" = f rest
     f (format:params) = check format params
     f _ = return ()
 
-    countFormats string =
-        case string of
-            '%':'%':rest -> countFormats rest
-            '%':'(':rest -> 1 + countFormats (dropWhile (/= ')') rest)
-            '%':rest -> regexBasedCountFormats rest + countFormats (dropWhile (/= '%') rest)
-            _:rest -> countFormats rest
-            [] -> 0
-
-    regexBasedCountFormats rest =
-        maybe 1 (foldl (\acc group -> acc + (if group == "*" then 1 else 0)) 1) (matchRegex re rest)
-      where
-        -- constructed based on specifications in "man printf"
-        re = mkRegex "#?-?\\+? ?0?(\\*|\\d*).?(\\d*|\\*)[diouxXfFeEgGaAcsb]"
-        --            \____ _____/\___ ____/ \____ ____/\________ ________/
-        --                 V          V           V               V
-        --               flags    field width  precision   format character
-        -- field width and precision can be specified with a '*' instead of a digit,
-        -- in which case printf will accept one more argument for each '*' used
     check format more = do
         fromMaybe (return ()) $ do
             string <- getLiteralString format
-            let vars = countFormats string
-
-            return $ do
-                when (vars == 0 && more /= []) $
-                    err (getId format) 2182
-                        "This printf format string has no variables. Other arguments are ignored."
-
-                when (vars > 0
-                        && ((length more) `mod` vars /= 0 || null more)
-                        && all (not . mayBecomeMultipleArgs) more) $
-                    warn (getId format) 2183 $
-                        "This format string has " ++ show vars ++ " variables, but is passed " ++ show (length more) ++ " arguments."
+            let formats = getPrintfFormats string
+            let formatCount = length formats
+            let argCount = length more
 
+            return $
+                case () of
+                    () | argCount == 0 && formatCount == 0 ->
+                        return () -- This is fine
+                    () | formatCount == 0 && argCount > 0 ->
+                        err (getId format) 2182
+                            "This printf format string has no variables. Other arguments are ignored."
+                    () | any mayBecomeMultipleArgs more ->
+                        return () -- We don't know so trust the user
+                    () | argCount < formatCount && onlyTrailingTs formats argCount ->
+                        return () -- Allow trailing %()Ts since they use the current time
+                    () | argCount > 0 && argCount `mod` formatCount == 0 ->
+                        return () -- Great: a suitable number of arguments
+                    () ->
+                        warn (getId format) 2183 $
+                            "This format string has " ++ show formatCount ++ " variables, but is passed " ++ show argCount ++ " arguments."
 
         unless ('%' `elem` concat (oversimplify format) || isLiteral format) $
           info (getId format) 2059
               "Don't use variables in the printf format string. Use printf \"..%s..\" \"$foo\"."
+      where
+        onlyTrailingTs format argCount =
+            all (== 'T') $ drop argCount format
 
 
+prop_checkGetPrintfFormats1 = getPrintfFormats "%s" == "s"
+prop_checkGetPrintfFormats2 = getPrintfFormats "%0*s" == "*s"
+prop_checkGetPrintfFormats3 = getPrintfFormats "%(%s)T" == "T"
+prop_checkGetPrintfFormats4 = getPrintfFormats "%d%%%(%s)T" == "dT"
+prop_checkGetPrintfFormats5 = getPrintfFormats "%bPassed: %d, %bFailed: %d%b, Skipped: %d, %bErrored: %d%b\\n" == "bdbdbdbdb"
+getPrintfFormats = getFormats
+  where
+    -- Get the arguments in the string as a string of type characters,
+    -- e.g. "Hello %s" -> "s" and "%(%s)T %0*d\n" -> "T*d"
+    getFormats :: String -> String
+    getFormats string =
+        case string of
+            '%':'%':rest -> getFormats rest
+            '%':'(':rest ->
+                case dropWhile (/= ')') rest of
+                    ')':c:trailing -> c : getFormats trailing
+                    _ -> ""
+            '%':rest -> regexBasedGetFormats rest
+            _:rest -> getFormats rest
+            [] -> ""
+
+    regexBasedGetFormats rest =
+        case matchRegex re rest of
+            Just [width, precision, typ, rest] ->
+                (if width == "*" then "*" else "") ++
+                (if precision == "*" then "*" else "") ++
+                typ ++ getFormats rest
+            Nothing -> take 1 rest ++ getFormats rest
+      where
+        -- constructed based on specifications in "man printf"
+        re = mkRegex "#?-?\\+? ?0?(\\*|\\d*)\\.?(\\d*|\\*)([diouxXfFeEgGaAcsbq])(.*)"
+        --            \____ _____/\___ ____/   \____ ____/\_________ _________/ \ /
+        --                 V          V             V               V            V
+        --               flags    field width  precision   format character     rest
+        -- field width and precision can be specified with a '*' instead of a digit,
+        -- in which case printf will accept one more argument for each '*' used
 
 
 prop_checkUuoeCmd1 = verify checkUuoeCmd "echo $(date)"
@@ -748,7 +806,7 @@ prop_checkLocalScope2 = verifyNot checkLocalScope "f() { local foo=3; }"
 checkLocalScope = CommandCheck (Exactly "local") $ \t ->
     whenShell [Bash, Dash] $ do -- Ksh allows it, Sh doesn't support local
         path <- getPathM t
-        unless (any isFunction path) $
+        unless (any isFunctionLike path) $
             err (getId $ getCommandTokenOrThis t) 2168 "'local' is only valid in functions."
 
 prop_checkDeprecatedTempfile1 = verify checkDeprecatedTempfile "var=$(tempfile)"
@@ -873,7 +931,7 @@ checkCatastrophicRm = CommandCheck (Basename "rm") $ \t ->
     getPotentialPath = getLiteralStringExt f
       where
         f (T_Glob _ str) = return str
-        f (T_DollarBraced _ word) =
+        f (T_DollarBraced _ _ word) =
             let var = onlyLiteralString word in
                 -- This shouldn't handle non-colon cases.
                 if any (`isInfixOf` var) [":?", ":-", ":="]
@@ -1008,5 +1066,27 @@ checkSudoArgs = CommandCheck (Basename "sudo") f
     -- This mess is why ShellCheck prefers not to know.
     parseOpts = getBsdOpts "vAknSbEHPa:g:h:p:u:c:T:r:"
 
+prop_checkSourceArgs1 = verify checkSourceArgs "#!/bin/sh\n. script arg"
+prop_checkSourceArgs2 = verifyNot checkSourceArgs "#!/bin/sh\n. script"
+prop_checkSourceArgs3 = verifyNot checkSourceArgs "#!/bin/bash\n. script arg"
+checkSourceArgs = CommandCheck (Exactly ".") f
+  where
+    f t = whenShell [Sh, Dash] $
+        case arguments t of
+            (file:arg1:_) -> warn (getId arg1) 2240 $
+                "The dot command does not support arguments in sh/dash. Set them as variables."
+            _ -> return ()
+
+prop_checkChmodDashr1 = verify checkChmodDashr "chmod -r 0755 dir"
+prop_checkChmodDashr2 = verifyNot checkChmodDashr "chmod -R 0755 dir"
+prop_checkChmodDashr3 = verifyNot checkChmodDashr "chmod a-r dir"
+checkChmodDashr = CommandCheck (Basename "chmod") f
+  where
+    f t = mapM_ check $ arguments t
+    check t = potentially $ do
+        flag <- getLiteralString t
+        guard $ flag == "-r"
+        return $ warn (getId t) 2253 "Use -R to recurse, or explicitly a-r to remove read permissions."
+
 return []
 runTests =  $( [| $(forAllProperties) (quickCheckWithResult (stdArgs { maxSuccess = 1 }) ) |])

src/ShellCheck/Checks/Custom.hs

@@ -0,0 +1,21 @@
+{-
+    This empty file is provided for ease of patching in site specific checks.
+    However, there are no guarantees regarding compatibility between versions.
+-} 
+
+{-# LANGUAGE TemplateHaskell #-}
+module ShellCheck.Checks.Custom (checker, ShellCheck.Checks.Custom.runTests) where
+
+import ShellCheck.AnalyzerLib
+import Test.QuickCheck
+
+checker :: Parameters -> Checker
+checker params = Checker {
+    perScript = const $ return (),
+    perToken = const $ return ()
+  }
+
+prop_CustomTestsWork = True
+
+return []
+runTests = $quickCheckAll

src/ShellCheck/Checks/ShellSupport.hs

@@ -33,6 +33,7 @@ import Data.Char
 import Data.List
 import Data.Maybe
 import qualified Data.Map as Map
+import qualified Data.Set as Set
 import Test.QuickCheck.All (forAllProperties)
 import Test.QuickCheck.Test (quickCheckWithResult, stdArgs, maxSuccess)
 
@@ -136,6 +137,46 @@ prop_checkBashisms53= verifyNot checkBashisms "#!/bin/sh\nprintf -- -f\n"
 prop_checkBashisms54= verify checkBashisms "#!/bin/sh\nfoo+=bar"
 prop_checkBashisms55= verify checkBashisms "#!/bin/sh\necho ${@%foo}"
 prop_checkBashisms56= verifyNot checkBashisms "#!/bin/sh\necho ${##}"
+prop_checkBashisms57= verifyNot checkBashisms "#!/bin/dash\nulimit -c 0"
+prop_checkBashisms58= verify checkBashisms "#!/bin/sh\nulimit -c 0"
+prop_checkBashisms59 = verify checkBashisms "#!/bin/sh\njobs -s"
+prop_checkBashisms60 = verifyNot checkBashisms "#!/bin/sh\njobs -p"
+prop_checkBashisms61 = verifyNot checkBashisms "#!/bin/sh\njobs -lp"
+prop_checkBashisms62 = verify checkBashisms "#!/bin/sh\nexport -f foo"
+prop_checkBashisms63 = verifyNot checkBashisms "#!/bin/sh\nexport -p"
+prop_checkBashisms64 = verify checkBashisms "#!/bin/sh\nreadonly -a"
+prop_checkBashisms65 = verifyNot checkBashisms "#!/bin/sh\nreadonly -p"
+prop_checkBashisms66 = verifyNot checkBashisms "#!/bin/sh\ncd -P ."
+prop_checkBashisms67 = verify checkBashisms "#!/bin/sh\ncd -P -e ."
+prop_checkBashisms68 = verify checkBashisms "#!/bin/sh\numask -p"
+prop_checkBashisms69 = verifyNot checkBashisms "#!/bin/sh\numask -S"
+prop_checkBashisms70 = verify checkBashisms "#!/bin/sh\ntrap -l"
+prop_checkBashisms71 = verify checkBashisms "#!/bin/sh\ntype -a ls"
+prop_checkBashisms72 = verifyNot checkBashisms "#!/bin/sh\ntype ls"
+prop_checkBashisms73 = verify checkBashisms "#!/bin/sh\nunset -n namevar"
+prop_checkBashisms74 = verifyNot checkBashisms "#!/bin/sh\nunset -f namevar"
+prop_checkBashisms75 = verifyNot checkBashisms "#!/bin/sh\necho \"-n foo\""
+prop_checkBashisms76 = verifyNot checkBashisms "#!/bin/sh\necho \"-ne foo\""
+prop_checkBashisms77 = verifyNot checkBashisms "#!/bin/sh\necho -Q foo"
+prop_checkBashisms78 = verify checkBashisms "#!/bin/sh\necho -ne foo"
+prop_checkBashisms79 = verify checkBashisms "#!/bin/sh\nhash -l"
+prop_checkBashisms80 = verifyNot checkBashisms "#!/bin/sh\nhash -r"
+prop_checkBashisms81 = verifyNot checkBashisms "#!/bin/dash\nhash -v"
+prop_checkBashisms82 = verifyNot checkBashisms "#!/bin/sh\nset -v +o allexport -o errexit -C"
+prop_checkBashisms83 = verifyNot checkBashisms "#!/bin/sh\nset --"
+prop_checkBashisms84 = verify checkBashisms "#!/bin/sh\nset -o pipefail"
+prop_checkBashisms85 = verify checkBashisms "#!/bin/sh\nset -B"
+prop_checkBashisms86 = verifyNot checkBashisms "#!/bin/dash\nset -o emacs"
+prop_checkBashisms87 = verify checkBashisms "#!/bin/sh\nset -o emacs"
+prop_checkBashisms88 = verifyNot checkBashisms "#!/bin/sh\nset -- wget -o foo 'https://some.url'"
+prop_checkBashisms89 = verifyNot checkBashisms "#!/bin/sh\nopts=$-\nset -\"$opts\""
+prop_checkBashisms90 = verifyNot checkBashisms "#!/bin/sh\nset -o \"$opt\""
+prop_checkBashisms91 = verify checkBashisms "#!/bin/sh\nwait -n"
+prop_checkBashisms92 = verify checkBashisms "#!/bin/sh\necho $((16#FF))"
+prop_checkBashisms93 = verify checkBashisms "#!/bin/sh\necho $(( 10#$(date +%m) ))"
+prop_checkBashisms94 = verify checkBashisms "#!/bin/sh\n[ -v var ]"
+prop_checkBashisms95 = verify checkBashisms "#!/bin/sh\necho $_"
+prop_checkBashisms96 = verifyNot checkBashisms "#!/bin/dash\necho $_"
 checkBashisms = ForShell [Sh, Dash] $ \t -> do
     params <- ask
     kludge params t
@@ -170,6 +211,8 @@ checkBashisms = ForShell [Sh, Dash] $ \t -> do
             warnMsg id "== in place of = is"
     bashism (TC_Binary id SingleBracket "=~" _ _) =
             warnMsg id "=~ regex matching is"
+    bashism (TC_Unary id SingleBracket "-v" _) =
+            warnMsg id "unary -v (in place of [ -n \"${var+x}\" ]) is"
     bashism (TC_Unary id _ "-a" _) =
             warnMsg id "unary -a in place of -e is"
     bashism (TA_Unary id op _)
@@ -194,7 +237,7 @@ checkBashisms = ForShell [Sh, Dash] $ \t -> do
     bashism t@(TA_Variable id str _) | isBashVariable str =
         warnMsg id $ str ++ " is"
 
-    bashism t@(T_DollarBraced id token) = do
+    bashism t@(T_DollarBraced id _ token) = do
         mapM_ check expansion
         when (isBashVariable var) $
                     warnMsg id $ var ++ " is"
@@ -222,20 +265,71 @@ checkBashisms = ForShell [Sh, Dash] $ \t -> do
         warnMsg id "`<file` to read files is"
 
     bashism t@(T_SimpleCommand _ _ (cmd:arg:_))
-        | t `isCommand` "echo" && "-" `isPrefixOf` argString =
-            unless ("--" `isPrefixOf` argString) $ -- echo "-----"
-                if isDash
-                then
-                    when (argString /= "-n") $
-                        warnMsg (getId arg) "echo flags besides -n"
-                else
-                    warnMsg (getId arg) "echo flags are"
-      where argString = concat $ oversimplify arg
+        | t `isCommand` "echo" && argString `matches` flagRegex =
+            if isDash
+            then
+                when (argString /= "-n") $
+                    warnMsg (getId arg) "echo flags besides -n"
+            else
+                warnMsg (getId arg) "echo flags are"
+      where
+          argString = concat $ oversimplify arg
+          flagRegex = mkRegex "^-[eEsn]+$"
+
     bashism t@(T_SimpleCommand _ _ (cmd:arg:_))
         | t `isCommand` "exec" && "-" `isPrefixOf` concat (oversimplify arg) =
             warnMsg (getId arg) "exec flags are"
     bashism t@(T_SimpleCommand id _ _)
         | t `isCommand` "let" = warnMsg id "'let' is"
+    bashism t@(T_SimpleCommand _ _ (cmd:args))
+        | t `isCommand` "set" = unless isDash $
+            checkOptions $ getLiteralArgs args
+      where
+        -- Get the literal options from a list of arguments,
+        -- up until the first non-literal one
+        getLiteralArgs :: [Token] -> [(Id, String)]
+        getLiteralArgs (first:rest) = fromMaybe [] $ do
+            str <- getLiteralString first
+            return $ (getId first, str) : getLiteralArgs rest
+        getLiteralArgs [] = []
+
+        -- Check a flag-option pair (such as -o errexit)
+        checkOptions (flag@(fid,flag') : opt@(oid,opt') : rest)
+            | flag' `matches` oFlagRegex = do
+                when (opt' `notElem` longOptions) $
+                  warnMsg oid $ "set option " <> opt' <> " is"
+                checkFlags (flag:rest)
+            | otherwise = checkFlags (flag:opt:rest)
+        checkOptions (flag:rest) = checkFlags (flag:rest)
+        checkOptions _           = return ()
+
+        -- Check that each option in a sequence of flags
+        -- (such as -aveo) is valid
+        checkFlags (flag@(fid, flag'):rest)
+            | startsOption flag' = do
+                unless (flag' `matches` validFlagsRegex) $
+                  forM_ (tail flag') $ \letter ->
+                    when (letter `notElem` optionsSet) $
+                      warnMsg fid $ "set flag " <> ('-':letter:" is")
+                checkOptions rest
+            | beginsWithDoubleDash flag' = do
+                warnMsg fid $ "set flag " <> flag' <> " is"
+                checkOptions rest
+            -- Either a word that doesn't start with a dash, or simply '--',
+            -- so stop checking.
+            | otherwise = return ()
+        checkFlags [] = return ()
+
+        options              = "abCefhmnuvxo"
+        optionsSet           = Set.fromList options
+        startsOption         = (`matches` mkRegex "^(\\+|-[^-])")
+        oFlagRegex           = mkRegex $ "^[-+][" <> options <> "]*o$"
+        validFlagsRegex      = mkRegex $ "^[-+]([" <> options <> "]+o?|o)$"
+        beginsWithDoubleDash = (`matches` mkRegex "^--.+$")
+        longOptions          = Set.fromList
+            [ "allexport", "errexit", "ignoreeof", "monitor", "noclobber"
+            , "noexec", "noglob", "nolog", "notify" , "nounset", "verbose"
+            , "vi", "xtrace" ]
 
     bashism t@(T_SimpleCommand id _ (cmd:rest)) =
         let name = fromMaybe "" $ getCommandName t
@@ -244,7 +338,8 @@ checkBashisms = ForShell [Sh, Dash] $ \t -> do
             when (name `elem` unsupportedCommands) $
                 warnMsg id $ "'" ++ name ++ "' is"
             potentially $ do
-                allowed <- Map.lookup name allowedFlags
+                allowed' <- Map.lookup name allowedFlags
+                allowed <- allowed'
                 (word, flag) <- listToMaybe $
                     filter (\x -> (not . null . snd $ x) && snd x `notElem` allowed) flags
                 return . warnMsg (getId word) $ name ++ " -" ++ flag ++ " is"
@@ -279,16 +374,28 @@ checkBashisms = ForShell [Sh, Dash] $ \t -> do
             "typeset"
             ] ++ if not isDash then ["local"] else []
         allowedFlags = Map.fromList [
-            ("exec", []),
-            ("export", ["-p"]),
-            ("printf", []),
-            ("read", if isDash then ["r", "p"] else ["r"]),
-            ("ulimit", ["f"])
+            ("cd", Just ["L", "P"]),
+            ("exec", Just []),
+            ("export", Just ["p"]),
+            ("hash", Just $ if isDash then ["r", "v"] else ["r"]),
+            ("jobs", Just ["l", "p"]),
+            ("printf", Just []),
+            ("read", Just $ if isDash then ["r", "p"] else ["r"]),
+            ("readonly", Just ["p"]),
+            ("trap", Just []),
+            ("type", Just []),
+            ("ulimit", if isDash then Nothing else Just ["f"]),
+            ("umask", Just ["S"]),
+            ("unset", Just ["f", "v"]),
+            ("wait", Just [])
             ]
     bashism t@(T_SourceCommand id src _) =
         let name = fromMaybe "" $ getCommandName src
-        in do
-            when (name == "source") $ warnMsg id "'source' in place of '.' is"
+        in when (name == "source") $ warnMsg id "'source' in place of '.' is"
+    bashism (TA_Expansion _ (T_Literal id str : _)) | str `matches` radix =
+        when (str `matches` radix) $ warnMsg id "arithmetic base conversion is"
+      where
+        radix = mkRegex "^[0-9]+#"
     bashism _ = return ()
 
     varChars="_0-9a-zA-Z"
@@ -303,10 +410,11 @@ checkBashisms = ForShell [Sh, Dash] $ \t -> do
         ]
     bashVars = [
         "OSTYPE", "MACHTYPE", "HOSTTYPE", "HOSTNAME",
-        "DIRSTACK", "EUID", "UID", "SHLVL", "PIPESTATUS", "SHELLOPTS"
+        "DIRSTACK", "EUID", "UID", "SHLVL", "PIPESTATUS", "SHELLOPTS",
+        "_"
         ]
     bashDynamicVars = [ "RANDOM", "SECONDS" ]
-    dashVars = [ ]
+    dashVars = [ "_" ]
     isBashVariable var =
         (var `elem` bashDynamicVars
             || var `elem` bashVars && not (isAssigned var))
@@ -318,31 +426,45 @@ checkBashisms = ForShell [Sh, Dash] $ \t -> do
                 _ -> False
 
 prop_checkEchoSed1 = verify checkEchoSed "FOO=$(echo \"$cow\" | sed 's/foo/bar/g')"
+prop_checkEchoSed1b= verify checkEchoSed "FOO=$(sed 's/foo/bar/g' <<< \"$cow\")"
 prop_checkEchoSed2 = verify checkEchoSed "rm $(echo $cow | sed -e 's,foo,bar,')"
+prop_checkEchoSed2b= verify checkEchoSed "rm $(sed -e 's,foo,bar,' <<< $cow)"
 checkEchoSed = ForShell [Bash, Ksh] f
   where
+    f (T_Redirecting id lefts r) =
+        when (any redirectHereString lefts) $
+            checkSed id rcmd
+      where
+        redirectHereString :: Token -> Bool
+        redirectHereString t = case t of
+            (T_FdRedirect _ _ T_HereString{}) -> True
+            _                                 -> False
+        rcmd = oversimplify r
+
     f (T_Pipeline id _ [a, b]) =
         when (acmd == ["echo", "${VAR}"]) $
-            case bcmd of
-                ["sed", v] -> checkIn v
-                ["sed", "-e", v] -> checkIn v
-                _ -> return ()
+            checkSed id bcmd
       where
-        -- This should have used backreferences, but TDFA doesn't support them
-        sedRe = mkRegex "^s(.)([^\n]*)g?$"
-        isSimpleSed s = fromMaybe False $ do
-            [first,rest] <- matchRegex sedRe s
-            let delimiters = filter (== head first) rest
-            guard $ length delimiters == 2
-            return True
-
         acmd = oversimplify a
         bcmd = oversimplify b
-        checkIn s =
-            when (isSimpleSed s) $
-                style id 2001 "See if you can use ${variable//search/replace} instead."
+
     f _ = return ()
 
+    checkSed id ["sed", v]       = checkIn id v
+    checkSed id ["sed", "-e", v] = checkIn id v
+    checkSed _ _                 = return ()
+
+    -- This should have used backreferences, but TDFA doesn't support them
+    sedRe = mkRegex "^s(.)([^\n]*)g?$"
+    isSimpleSed s = fromMaybe False $ do
+        [first,rest] <- matchRegex sedRe s
+        let delimiters = filter (== head first) rest
+        guard $ length delimiters == 2
+        return True
+    checkIn id s =
+        when (isSimpleSed s) $
+            style id 2001 "See if you can use ${variable//search/replace} instead."
+
 
 prop_checkBraceExpansionVars1 = verify checkBraceExpansionVars "echo {1..$n}"
 prop_checkBraceExpansionVars2 = verifyNot checkBraceExpansionVars "echo {1,3,$n}"

src/ShellCheck/Data.hs

@@ -36,13 +36,29 @@ internalVariables = [
 
     -- Ksh
     , ".sh.version"
+
+    -- shflags
+    , "FLAGS_ARGC", "FLAGS_ARGV", "FLAGS_ERROR", "FLAGS_FALSE", "FLAGS_HELP",
+    "FLAGS_PARENT", "FLAGS_RESERVED", "FLAGS_TRUE", "FLAGS_VERSION",
+    "flags_error", "flags_return"
   ]
 
-variablesWithoutSpaces = [
-    "$", "-", "?", "!", "#",
+specialVariablesWithoutSpaces = [
+    "$", "-", "?", "!", "#"
+  ]
+variablesWithoutSpaces = specialVariablesWithoutSpaces ++ [
     "BASHPID", "BASH_ARGC", "BASH_LINENO", "BASH_SUBSHELL", "EUID", "LINENO",
     "OPTIND", "PPID", "RANDOM", "SECONDS", "SHELLOPTS", "SHLVL", "UID",
     "COLUMNS", "HISTFILESIZE", "HISTSIZE", "LINES"
+
+    -- shflags
+    , "FLAGS_ERROR", "FLAGS_FALSE", "FLAGS_TRUE"
+  ]
+
+specialVariables = specialVariablesWithoutSpaces ++ ["@", "*"]
+
+unbracedVariables = specialVariables ++ [
+    "0", "1", "2", "3", "4", "5", "6", "7", "8", "9"
   ]
 
 arrayVariables = [
@@ -109,6 +125,7 @@ shellForExecutable name =
     case name of
         "sh"    -> return Sh
         "bash"  -> return Bash
+        "bats"  -> return Bash
         "dash"  -> return Dash
         "ash"   -> return Dash -- There's also a warning for this.
         "ksh"   -> return Ksh

src/ShellCheck/Fixer.hs

@@ -0,0 +1,409 @@
+{-
+    Copyright 2018-2019 Vidar Holen, Ng Zhi An
+
+    This file is part of ShellCheck.
+    https://www.shellcheck.net
+
+    ShellCheck is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    ShellCheck is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+-}
+
+{-# LANGUAGE TemplateHaskell #-}
+module ShellCheck.Fixer (applyFix, removeTabStops, mapPositions, Ranged(..), runTests) where
+
+import ShellCheck.Interface
+import Control.Monad.State
+import Data.Array
+import Data.List
+import Data.Semigroup
+import GHC.Exts (sortWith)
+import Test.QuickCheck
+
+-- The Ranged class is used for types that has a start and end position.
+class Ranged a where
+    start   :: a -> Position
+    end     :: a -> Position
+    overlap :: a -> a -> Bool
+    overlap x y =
+        (yStart >= xStart && yStart < xEnd) || (yStart < xStart && yEnd > xStart)
+        where
+            yStart = start y
+            yEnd = end y
+            xStart = start x
+            xEnd = end x
+    -- Set a new start and end position on a Ranged
+    setRange :: (Position, Position) -> a -> a
+
+-- Tests auto-verify that overlap commutes
+assertOverlap x y = overlap x y && overlap y x
+assertNoOverlap x y = not (overlap x y) && not (overlap y x)
+
+prop_overlap_contiguous = assertNoOverlap
+        (tFromStart 10 12 "foo" 1)
+        (tFromStart 12 14 "bar" 2)
+
+prop_overlap_adjacent_zerowidth = assertNoOverlap
+        (tFromStart 3 3 "foo" 1)
+        (tFromStart 3 3 "bar" 2)
+
+prop_overlap_enclosed = assertOverlap
+        (tFromStart 3 5 "foo" 1)
+        (tFromStart 1 10 "bar" 2)
+
+prop_overlap_partial = assertOverlap
+        (tFromStart 1 5 "foo" 1)
+        (tFromStart 3 7 "bar" 2)
+
+
+instance Ranged PositionedComment where
+    start = pcStartPos
+    end = pcEndPos
+    setRange (s, e) pc = pc {
+        pcStartPos = s,
+        pcEndPos = e
+    }
+
+instance Ranged Replacement where
+    start = repStartPos
+    end   = repEndPos
+    setRange (s, e) r = r {
+        repStartPos = s,
+        repEndPos = e
+    }
+
+-- The Monoid instance for Fix merges fixes that do not conflict.
+-- TODO: Make an efficient 'mconcat'
+instance Monoid Fix where
+    mempty = newFix
+    mappend = (<>)
+
+instance Semigroup Fix where
+    f1 <> f2 =
+        -- FIXME: This might need to also discard adjacent zero-width ranges for
+        --        when two fixes change the same AST node, e.g. `foo` -> "$(foo)"
+        if or [ r2 `overlap` r1 | r1 <- fixReplacements f1, r2 <- fixReplacements f2 ]
+        then f1
+        else newFix {
+            fixReplacements = fixReplacements f1 ++ fixReplacements f2
+            }
+
+-- Conveniently apply a transformation to positions in a Fix
+mapPositions :: (Position -> Position) -> Fix -> Fix
+mapPositions f = adjustFix
+  where
+    adjustReplacement rep =
+        rep {
+            repStartPos = f $ repStartPos rep,
+            repEndPos = f $ repEndPos rep
+        }
+    adjustFix fix =
+        fix {
+            fixReplacements = map adjustReplacement $ fixReplacements fix
+        }
+
+-- Rewrite a Ranged from a tabstop of 8 to 1
+removeTabStops :: Ranged a => a -> Array Int String -> a
+removeTabStops range ls =
+    let startColumn = realignColumn lineNo colNo range
+        endColumn = realignColumn endLineNo endColNo range
+        startPosition = (start range) { posColumn = startColumn }
+        endPosition = (end range) { posColumn = endColumn } in
+    setRange (startPosition, endPosition) range
+  where
+    realignColumn lineNo colNo c =
+      if lineNo c > 0 && lineNo c <= fromIntegral (length ls)
+      then real (ls ! fromIntegral (lineNo c)) 0 0 (colNo c)
+      else colNo c
+    real _ r v target | target <= v = r
+    -- hit this case at the end of line, and if we don't hit the target
+    -- return real + (target - v)
+    real [] r v target = r + (target - v)
+    real ('\t':rest) r v target = real rest (r+1) (v + 8 - (v `mod` 8)) target
+    real (_:rest) r v target = real rest (r+1) (v+1) target
+    lineNo = posLine . start
+    endLineNo = posLine . end
+    colNo = posColumn . start
+    endColNo = posColumn . end
+
+
+-- A replacement that spans multiple line is applied by:
+-- 1. merging the affected lines into a single string using `unlines`
+-- 2. apply the replacement as if it only spanned a single line
+-- The tricky part is adjusting the end column of the replacement
+-- (the end line doesn't matter because there is only one line)
+--
+--   aaS  <--- start of replacement (row 1 column 3)
+--   bbbb
+--   cEc
+--    \------- end of replacement (row 3 column 2)
+--
+-- a flattened string will look like:
+--
+--   "aaS\nbbbb\ncEc\n"
+--
+-- The column of E has to be adjusted by:
+-- 1. lengths of lines to be replaced, except the end row itself
+-- 2. end column of the replacement
+-- 3. number of '\n' by `unlines`
+multiToSingleLine :: [Fix] -> Array Int String -> ([Fix], String)
+multiToSingleLine fixes lines =
+    (map (mapPositions adjust) fixes, unlines $ elems lines)
+  where
+    -- A prefix sum tree from line number to column shift.
+    -- FIXME: The tree will be totally unbalanced.
+    shiftTree :: PSTree Int
+    shiftTree =
+        foldl (\t (n,s) -> addPSValue (n+1) (length s + 1) t) newPSTree $
+            assocs lines
+    singleString = unlines $ elems lines
+    adjust pos =
+        pos {
+            posLine = 1,
+            posColumn = (posColumn pos) +
+                (fromIntegral $ getPrefixSum (fromIntegral $ posLine pos) shiftTree)
+        }
+
+-- Apply a fix and return resulting lines.
+-- The number of lines can increase or decrease with no obvious mapping back, so
+-- the function does not return an array.
+applyFix :: Fix -> Array Int String -> [String]
+applyFix fix fileLines =
+    let
+        untabbed = fix {
+            fixReplacements =
+                map (\c -> removeTabStops c fileLines) $
+                    fixReplacements fix
+            }
+        (adjustedFixes, singleLine) = multiToSingleLine [untabbed] fileLines
+    in
+        lines . runFixer $ applyFixes2 adjustedFixes singleLine
+
+
+-- start and end comes from pos, which is 1 based
+prop_doReplace1 = doReplace 0 0 "1234" "A" == "A1234" -- technically not valid
+prop_doReplace2 = doReplace 1 1 "1234" "A" == "A1234"
+prop_doReplace3 = doReplace 1 2 "1234" "A" == "A234"
+prop_doReplace4 = doReplace 3 3 "1234" "A" == "12A34"
+prop_doReplace5 = doReplace 4 4 "1234" "A" == "123A4"
+prop_doReplace6 = doReplace 5 5 "1234" "A" == "1234A"
+doReplace start end o r =
+    let si = fromIntegral (start-1)
+        ei = fromIntegral (end-1)
+        (x, xs) = splitAt si o
+        (y, z) = splitAt (ei - si) xs
+    in
+    x ++ r ++ z
+
+-- Fail if the 'expected' string is not result when applying 'fixes' to 'original'.
+testFixes :: String -> String -> [Fix] -> Bool
+testFixes expected original fixes =
+    actual == expected
+  where
+    actual = runFixer (applyFixes2 fixes original)
+
+
+-- A Fixer allows doing repeated modifications of a string where each
+-- replacement automatically accounts for shifts from previous ones.
+type Fixer a =  State (PSTree Int) a
+
+-- Apply a single replacement using its indices into the original string.
+-- It does not handle multiple lines, all line indices must be 1.
+applyReplacement2 :: Replacement -> String -> Fixer String
+applyReplacement2 rep string = do
+    tree <- get
+    let transform pos = pos + getPrefixSum pos tree
+    let originalPos = (repStartPos rep, repEndPos rep)
+        (oldStart, oldEnd) = tmap (fromInteger . posColumn) originalPos
+        (newStart, newEnd) = tmap transform (oldStart, oldEnd)
+
+    let (l1, l2) = tmap posLine originalPos in
+        when (l1 /= 1 || l2 /= 1) $
+            error "ShellCheck internal error, please report: bad cross-line fix"
+
+    let replacer = repString rep
+    let shift = (length replacer) - (oldEnd - oldStart)
+    let insertionPoint =
+          case repInsertionPoint rep of
+              InsertBefore -> oldStart
+              InsertAfter  -> oldEnd+1
+    put $ addPSValue insertionPoint shift tree
+
+    return $ doReplace newStart newEnd string replacer
+  where
+    tmap f (a,b) = (f a, f b)
+
+-- Apply a list of Replacements in the correct order
+applyReplacements2 :: [Replacement] -> String -> Fixer String
+applyReplacements2 reps str =
+    foldM (flip applyReplacement2) str $
+        reverse $ sortWith repPrecedence reps
+
+-- Apply all fixes with replacements in the correct order
+applyFixes2 :: [Fix] -> String -> Fixer String
+applyFixes2 fixes = applyReplacements2 (concatMap fixReplacements fixes)
+
+-- Get the final value of a Fixer.
+runFixer :: Fixer a -> a
+runFixer f = evalState f newPSTree
+
+
+
+-- A Prefix Sum Tree that lets you look up the sum of values at and below an index.
+-- It's implemented essentially as a Fenwick tree without the bit-based balancing.
+-- The last Num is the sum of the left branch plus current element.
+data PSTree n = PSBranch n (PSTree n) (PSTree n) n | PSLeaf
+    deriving (Show)
+
+newPSTree :: Num n => PSTree n
+newPSTree = PSLeaf
+
+-- Get the sum of values whose keys are <= 'target'
+getPrefixSum :: (Ord n, Num n) => n -> PSTree n -> n
+getPrefixSum = f 0
+  where
+    f sum _ PSLeaf = sum
+    f sum target (PSBranch pivot left right cumulative) =
+        case () of
+            _ | target < pivot -> f sum target left
+            _ | target > pivot -> f (sum+cumulative) target right
+            _ -> sum+cumulative
+
+-- Add a value to the Prefix Sum tree at the given index.
+-- Values accumulate: addPSValue 42 2 . addPSValue 42 3 == addPSValue 42 5
+addPSValue :: (Ord n, Num n) => n -> n -> PSTree n -> PSTree n
+addPSValue key value tree = if value == 0 then tree else f tree
+  where
+    f PSLeaf = PSBranch key PSLeaf PSLeaf value
+    f (PSBranch pivot left right sum) =
+        case () of
+            _ | key < pivot -> PSBranch pivot (f left) right (sum + value)
+            _ | key > pivot -> PSBranch pivot left (f right) sum
+            _ -> PSBranch pivot left right (sum + value)
+
+prop_pstreeSumsCorrectly kvs targets =
+  let
+    -- Trivial O(n * m) implementation
+    dumbPrefixSums :: [(Int, Int)] -> [Int] -> [Int]
+    dumbPrefixSums kvs targets =
+        let prefixSum target = sum . map snd . filter (\(k,v) -> k <= target) $ kvs
+        in map prefixSum targets
+    -- PSTree O(n * log m) implementation
+    smartPrefixSums :: [(Int, Int)] -> [Int] -> [Int]
+    smartPrefixSums kvs targets =
+        let tree = foldl (\tree (pos, shift) -> addPSValue pos shift tree) PSLeaf kvs
+        in map (\x -> getPrefixSum x tree) targets
+  in smartPrefixSums kvs targets == dumbPrefixSums kvs targets
+
+
+-- Semi-convenient functions for constructing tests.
+testFix :: [Replacement] -> Fix
+testFix list = newFix {
+        fixReplacements = list
+    }
+
+tFromStart :: Int -> Int -> String -> Int -> Replacement
+tFromStart start end repl order =
+    newReplacement {
+        repStartPos = newPosition {
+            posLine = 1,
+            posColumn = fromIntegral start
+        },
+        repEndPos = newPosition {
+            posLine = 1,
+            posColumn = fromIntegral end
+        },
+        repString = repl,
+        repPrecedence = order,
+        repInsertionPoint = InsertAfter
+    }
+
+tFromEnd start end repl order =
+    (tFromStart start end repl order) {
+        repInsertionPoint = InsertBefore
+    }
+
+prop_simpleFix1 = testFixes "hello world" "hell world" [
+    testFix [
+        tFromEnd 5 5 "o" 1
+    ]]
+
+prop_anchorsLeft = testFixes "-->foobar<--" "--><--" [
+    testFix [
+        tFromStart 4 4 "foo" 1,
+        tFromStart 4 4 "bar" 2
+    ]]
+
+prop_anchorsRight = testFixes "-->foobar<--" "--><--" [
+    testFix [
+        tFromEnd 4 4 "bar" 1,
+        tFromEnd 4 4 "foo" 2
+    ]]
+
+prop_anchorsBoth1 = testFixes "-->foobar<--" "--><--" [
+    testFix [
+        tFromStart 4 4 "bar" 2,
+        tFromEnd 4 4 "foo" 1
+    ]]
+
+prop_anchorsBoth2 = testFixes "-->foobar<--" "--><--" [
+    testFix [
+        tFromEnd 4 4 "foo" 2,
+        tFromStart 4 4 "bar" 1
+    ]]
+
+prop_composeFixes1 = testFixes "cd \"$1\" || exit" "cd $1" [
+    testFix [
+        tFromStart 4 4 "\"" 10,
+        tFromEnd   6 6 "\"" 10
+    ],
+    testFix [
+        tFromEnd 6 6 " || exit" 5
+    ]]
+
+prop_composeFixes2 = testFixes "$(\"$1\")" "`$1`" [
+    testFix [
+        tFromStart 1 2 "$(" 5,
+        tFromEnd   4 5 ")" 5
+    ],
+    testFix [
+        tFromStart 2 2 "\"" 10,
+        tFromEnd 4 4 "\"" 10
+    ]]
+
+prop_composeFixes3 = testFixes "(x)[x]" "xx" [
+    testFix [
+        tFromStart 1 1 "(" 4,
+        tFromEnd   2 2 ")" 3,
+        tFromStart 2 2 "[" 2,
+        tFromEnd   3 3 "]" 1
+    ]]
+
+prop_composeFixes4 = testFixes "(x)[x]" "xx" [
+    testFix [
+        tFromStart 1 1 "(" 4,
+        tFromStart 2 2 "[" 3,
+        tFromEnd   2 2 ")" 2,
+        tFromEnd   3 3 "]" 1
+    ]]
+
+prop_composeFixes5 = testFixes "\"$(x)\"" "`x`" [
+    testFix [
+        tFromStart 1 2 "$(" 2,
+        tFromEnd   3 4 ")"  2,
+        tFromStart 1 1 "\"" 1,
+        tFromEnd   4 4 "\"" 1
+    ]]
+
+
+return []
+runTests = $quickCheckAll

src/ShellCheck/Formatter/CheckStyle.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net

src/ShellCheck/Formatter/Diff.hs

@@ -0,0 +1,255 @@
+{-
+    Copyright 2019 Vidar 'koala_man' Holen
+
+    This file is part of ShellCheck.
+    https://www.shellcheck.net
+
+    ShellCheck is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    ShellCheck is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+-}
+{-# LANGUAGE TemplateHaskell #-}
+module ShellCheck.Formatter.Diff (format, ShellCheck.Formatter.Diff.runTests) where
+
+import ShellCheck.Interface
+import ShellCheck.Fixer
+import ShellCheck.Formatter.Format
+
+import Control.Monad
+import Data.Algorithm.Diff
+import Data.Array
+import Data.IORef
+import Data.List
+import qualified Data.Monoid as Monoid
+import Data.Maybe
+import qualified Data.Map as M
+import GHC.Exts (sortWith)
+import System.IO
+import System.FilePath
+
+import Test.QuickCheck
+
+import Debug.Trace
+ltt x = trace (show x) x
+
+format :: FormatterOptions -> IO Formatter
+format options = do
+    didOutput <- newIORef False
+    shouldColor <- shouldOutputColor (foColorOption options)
+    let color = if shouldColor then colorize else nocolor
+    return Formatter {
+        header = return (),
+        footer = checkFooter didOutput color,
+        onFailure = reportFailure color,
+        onResult  = reportResult didOutput color
+    }
+
+
+contextSize = 3
+red = 31
+green = 32
+yellow = 33
+cyan = 36
+bold = 1
+
+nocolor n = id
+colorize n s = (ansi n) ++ s ++ (ansi 0)
+ansi n = "\x1B[" ++ show n ++ "m"
+
+printErr :: ColorFunc -> String -> IO ()
+printErr color = hPutStrLn stderr . color bold . color red
+reportFailure color file msg = printErr color $ file ++ ": " ++ msg
+
+checkFooter didOutput color = do
+    output <- readIORef didOutput
+    unless output $
+            printErr color "Issues were detected, but none were auto-fixable. Use another format to see them."
+
+type ColorFunc = (Int -> String -> String)
+data LFStatus = LinefeedMissing | LinefeedOk
+data DiffDoc a = DiffDoc String LFStatus [DiffRegion a]
+data DiffRegion a = DiffRegion (Int, Int) (Int, Int) [Diff a]
+
+reportResult :: (IORef Bool) -> ColorFunc -> CheckResult -> SystemInterface IO -> IO ()
+reportResult didOutput color result sys = do
+    let comments = crComments result
+    let suggestedFixes = mapMaybe pcFix comments
+    let fixmap = buildFixMap suggestedFixes
+    mapM_ output $ M.toList fixmap
+  where
+    output (name, fix) = do
+        file <- (siReadFile sys) name
+        case file of
+            Right contents -> do
+                putStrLn $ formatDoc color $ makeDiff name contents fix
+                writeIORef didOutput True
+            Left msg -> reportFailure color name msg
+
+hasTrailingLinefeed str =
+    case str of
+        [] -> True
+        _ -> last str == '\n'
+
+coversLastLine regions =
+    case regions of
+        [] -> False
+        _ -> (fst $ last regions)
+
+-- TODO: Factor this out into a unified diff library because we're doing a lot
+-- of the heavy lifting anyways.
+makeDiff :: String -> String -> Fix -> DiffDoc String
+makeDiff name contents fix = do
+    let hunks = groupDiff $ computeDiff contents fix
+    let lf = if coversLastLine hunks && not (hasTrailingLinefeed contents)
+             then LinefeedMissing
+             else LinefeedOk
+    DiffDoc name lf $ findRegions hunks
+
+computeDiff :: String -> Fix -> [Diff String]
+computeDiff contents fix =
+    let old = lines contents
+        array = listArray (1, fromIntegral $ (length old)) old
+        new = applyFix fix array
+    in getDiff old new
+
+-- Group changes into hunks
+groupDiff :: [Diff a] -> [(Bool, [Diff a])]
+groupDiff = filter (\(_, l) -> not (null l)) . hunt []
+  where
+    -- Churn through 'Both's until we find a difference
+    hunt current [] = [(False, reverse current)]
+    hunt current (x@Both {}:rest) = hunt (x:current) rest
+    hunt current list =
+        let (context, previous) = splitAt contextSize current
+        in (False, reverse previous) : gather context 0 list
+
+    -- Pick out differences until we find a run of Both's
+    gather current n [] =
+        let (extras, patch) = splitAt (max 0 $ n - contextSize) current
+        in [(True, reverse patch), (False, reverse extras)]
+
+    gather current n list@(Both {}:_) | n == contextSize*2 =
+        let (context, previous) = splitAt contextSize current
+        in (True, reverse previous) : hunt context list
+
+    gather current n (x@Both {}:rest) = gather (x:current) (n+1) rest
+    gather current n (x:rest) = gather (x:current) 0 rest
+
+-- Get line numbers for hunks
+findRegions :: [(Bool, [Diff String])] -> [DiffRegion String]
+findRegions = find' 1 1
+  where
+    find' _ _ [] = []
+    find' left right ((output, run):rest) =
+        let (dl, dr) = countDelta run
+            remainder = find' (left+dl) (right+dr) rest
+        in
+            if output
+            then DiffRegion (left, dl) (right, dr) run : remainder
+            else remainder
+
+-- Get left/right line counts for a hunk
+countDelta :: [Diff a] -> (Int, Int)
+countDelta = count' 0 0
+  where
+    count' left right [] = (left, right)
+    count' left right (x:rest) =
+        case x of
+            Both {} -> count' (left+1) (right+1) rest
+            First {} -> count' (left+1) right rest
+            Second {} -> count' left (right+1) rest
+
+formatRegion :: ColorFunc -> LFStatus -> DiffRegion String -> String
+formatRegion color lf (DiffRegion left right diffs) =
+    let header = color cyan ("@@ -" ++ (tup left) ++ " +" ++ (tup right) ++" @@")
+    in
+        unlines $ header : reverse (getStrings lf (reverse diffs))
+  where
+    noLF = "\\ No newline at end of file"
+
+    getStrings LinefeedOk list = map format list
+    getStrings LinefeedMissing list@((Both _ _):_) = noLF : map format list
+    getStrings LinefeedMissing list@((First _):_) = noLF : map format list
+    getStrings LinefeedMissing (last:rest) = format last : getStrings LinefeedMissing rest
+
+    tup (a,b) = (show a) ++ "," ++ (show b)
+    format (Both x _) = ' ':x
+    format (First x) = color red $ '-':x
+    format (Second x) = color green $ '+':x
+
+splitLast [] = ([], [])
+splitLast x =
+    let (last, rest) = splitAt 1 $ reverse x
+    in (reverse rest, last)
+
+formatDoc color (DiffDoc name lf regions) =
+    let (most, last) = splitLast regions
+    in
+          (color bold $ "--- " ++ ("a" </> name)) ++ "\n" ++
+          (color bold $ "+++ " ++ ("b" </> name)) ++ "\n" ++
+          concatMap (formatRegion color LinefeedOk) most ++
+          concatMap (formatRegion color lf) last
+
+-- Create a Map from filename to Fix
+buildFixMap :: [Fix] -> M.Map String Fix
+buildFixMap fixes = perFile
+  where
+    splitFixes = concatMap splitFixByFile fixes
+    perFile = groupByMap (posFile . repStartPos . head . fixReplacements) splitFixes
+
+-- There are currently no multi-file fixes, but let's handle it anyways
+splitFixByFile :: Fix -> [Fix]
+splitFixByFile fix = map makeFix $ groupBy sameFile (fixReplacements fix)
+  where
+    sameFile rep1 rep2 = (posFile $ repStartPos rep1) == (posFile $ repStartPos rep2)
+    makeFix reps = newFix { fixReplacements = reps }
+
+groupByMap :: (Ord k, Monoid v) => (v -> k) -> [v] -> M.Map k v
+groupByMap f = M.fromListWith Monoid.mappend . map (\x -> (f x, x))
+
+-- For building unit tests
+b n = Both n n
+l = First
+r = Second
+
+prop_identifiesProperContext = groupDiff [b 1, b 2, b 3, b 4, l 5, b 6, b 7, b 8, b 9] ==
+    [(False, [b 1]), -- Omitted
+    (True, [b 2, b 3, b 4, l 5, b 6, b 7, b 8]), -- A change with three lines of context
+    (False, [b 9])]  -- Omitted
+
+prop_includesContextFromStartIfNecessary = groupDiff [b 4, l 5, b 6, b 7, b 8, b 9] ==
+    [ -- Nothing omitted
+    (True, [b 4, l 5, b 6, b 7, b 8]), -- A change with three lines of context
+    (False, [b 9])]  -- Omitted
+
+prop_includesContextUntilEndIfNecessary = groupDiff [b 4, l 5] ==
+    [ -- Nothing omitted
+        (True, [b 4, l 5])
+    ] -- Nothing Omitted
+
+prop_splitsIntoMultipleHunks = groupDiff [l 1, b 1, b 2, b 3, b 4, b 5, b 6, b 7, r 8] ==
+    [ -- Nothing omitted
+        (True, [l 1, b 1, b 2, b 3]),
+        (False, [b 4]),
+        (True, [b 5, b 6, b 7, r 8])
+    ] -- Nothing Omitted
+
+prop_splitsIntoMultipleHunksUnlessTouching = groupDiff [l 1, b 1, b 2, b 3, b 4, b 5, b 6, r 7] ==
+    [
+        (True, [l 1, b 1, b 2, b 3, b 4, b 5, b 6, r 7])
+    ]
+
+prop_countDeltasWorks = countDelta [b 1, l 2, r 3, r 4, b 5] == (3,4)
+prop_countDeltasWorks2 = countDelta [] == (0,0)
+
+return []
+runTests = $quickCheckAll

src/ShellCheck/Formatter/Format.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -21,6 +21,13 @@ module ShellCheck.Formatter.Format where
 
 import ShellCheck.Data
 import ShellCheck.Interface
+import ShellCheck.Fixer
+
+import Control.Monad
+import Data.Array
+import Data.List
+import System.IO
+import System.Info
 
 -- A formatter that carries along an arbitrary piece of data
 data Formatter = Formatter {
@@ -50,21 +57,23 @@ severityText pc =
 makeNonVirtual comments contents =
     map fix comments
   where
-    ls = lines contents
-    fix c = c {
-        pcStartPos = (pcStartPos c) {
-            posColumn = realignColumn lineNo colNo c
-        }
-      , pcEndPos = (pcEndPos c) {
-            posColumn = realignColumn endLineNo endColNo c
-        }
+    list = lines contents
+    arr = listArray (1, length list) list
+    untabbedFix f = newFix {
+      fixReplacements = map (\r -> removeTabStops r arr) (fixReplacements f)
     }
-    realignColumn lineNo colNo c =
-      if lineNo c > 0 && lineNo c <= fromIntegral (length ls)
-      then real (ls !! fromIntegral (lineNo c - 1)) 0 0 (colNo c)
-      else colNo c
-    real _ r v target | target <= v = r
-    real [] r v _ = r -- should never happen
-    real ('\t':rest) r v target =
-        real rest (r+1) (v + 8 - (v `mod` 8)) target
-    real (_:rest) r v target = real rest (r+1) (v+1) target
+    fix c = (removeTabStops c arr) {
+      pcFix = fmap untabbedFix (pcFix c)
+    }
+
+
+shouldOutputColor :: ColorOption -> IO Bool
+shouldOutputColor colorOption = do
+    term <- hIsTerminalDevice stdout
+    let windows = "mingw" `isPrefixOf` os
+    let isUsableTty = term && not windows
+    let useColor = case colorOption of
+                       ColorAlways -> True
+                       ColorNever -> False
+                       ColorAuto -> isUsableTty
+    return useColor

src/ShellCheck/Formatter/GCC.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net

src/ShellCheck/Formatter/JSON.hs

@@ -1,6 +1,6 @@
 {-# LANGUAGE OverloadedStrings #-}
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -30,6 +30,7 @@ import GHC.Exts
 import System.IO
 import qualified Data.ByteString.Lazy.Char8 as BL
 
+format :: IO Formatter
 format = do
     ref <- newIORef []
     return Formatter {
@@ -45,11 +46,16 @@ instance ToJSON Replacement where
             end = repEndPos replacement
             str = repString replacement in
         object [
+          "precedence" .= repPrecedence replacement,
+          "insertionPoint"  .=
+            case repInsertionPoint replacement of
+                InsertBefore -> "beforeStart" :: String
+                InsertAfter  -> "afterEnd",
           "line" .= posLine start,
-          "endLine" .= posLine end,
           "column" .= posColumn start,
+          "endLine" .= posLine end,
           "endColumn" .= posColumn end,
-          "replaceWith" .= str
+          "replacement" .= str
         ]
 
 instance ToJSON PositionedComment where
@@ -91,8 +97,13 @@ instance ToJSON Fix where
         ]
 
 outputError file msg = hPutStrLn stderr $ file ++ ": " ++ msg
-collectResult ref result _ =
-    modifyIORef ref (\x -> crComments result ++ x)
+
+collectResult ref cr sys = mapM_ f groups
+  where
+    comments = crComments cr
+    groups = groupWith sourceFile comments
+    f :: [PositionedComment] -> IO ()
+    f group = modifyIORef ref (\x -> comments ++ x)
 
 finish ref = do
     list <- readIORef ref

src/ShellCheck/Formatter/JSON1.hs

@@ -0,0 +1,127 @@
+{-# LANGUAGE OverloadedStrings #-}
+{-
+    Copyright 2012-2019 Vidar Holen
+
+    This file is part of ShellCheck.
+    https://www.shellcheck.net
+
+    ShellCheck is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    ShellCheck is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+-}
+module ShellCheck.Formatter.JSON1 (format) where
+
+import ShellCheck.Interface
+import ShellCheck.Formatter.Format
+
+import Data.Aeson
+import Data.IORef
+import Data.Monoid
+import GHC.Exts
+import System.IO
+import qualified Data.ByteString.Lazy.Char8 as BL
+
+format :: IO Formatter
+format = do
+    ref <- newIORef []
+    return Formatter {
+        header = return (),
+        onResult = collectResult ref,
+        onFailure = outputError,
+        footer = finish ref
+    }
+
+data Json1Output = Json1Output {
+    comments :: [PositionedComment]
+    }
+
+instance ToJSON Json1Output where
+    toJSON result = object [
+        "comments" .= comments result
+        ]
+    toEncoding result = pairs (
+        "comments" .= comments result
+        )
+
+instance ToJSON Replacement where
+    toJSON replacement =
+        let start = repStartPos replacement
+            end = repEndPos replacement
+            str = repString replacement in
+        object [
+          "precedence" .= repPrecedence replacement,
+          "insertionPoint"  .=
+            case repInsertionPoint replacement of
+                InsertBefore -> "beforeStart" :: String
+                InsertAfter  -> "afterEnd",
+          "line" .= posLine start,
+          "column" .= posColumn start,
+          "endLine" .= posLine end,
+          "endColumn" .= posColumn end,
+          "replacement" .= str
+        ]
+
+instance ToJSON PositionedComment where
+  toJSON comment =
+    let start = pcStartPos comment
+        end = pcEndPos comment
+        c = pcComment comment in
+    object [
+      "file" .= posFile start,
+      "line" .= posLine start,
+      "endLine" .= posLine end,
+      "column" .= posColumn start,
+      "endColumn" .= posColumn end,
+      "level" .= severityText comment,
+      "code" .= cCode c,
+      "message" .= cMessage c,
+      "fix" .= pcFix comment
+    ]
+
+  toEncoding comment =
+    let start = pcStartPos comment
+        end = pcEndPos comment
+        c = pcComment comment in
+    pairs (
+         "file" .= posFile start
+      <> "line" .= posLine start
+      <> "endLine" .= posLine end
+      <> "column" .= posColumn start
+      <> "endColumn" .= posColumn end
+      <> "level" .= severityText comment
+      <> "code" .= cCode c
+      <> "message" .= cMessage c
+      <> "fix" .= pcFix comment
+    )
+
+instance ToJSON Fix where
+    toJSON fix = object [
+        "replacements" .= fixReplacements fix
+        ]
+
+outputError file msg = hPutStrLn stderr $ file ++ ": " ++ msg
+
+collectResult ref cr sys = mapM_ f groups
+  where
+    comments = crComments cr
+    groups = groupWith sourceFile comments
+    f :: [PositionedComment] -> IO ()
+    f group = do
+        let filename = sourceFile (head group)
+        result <- siReadFile sys filename
+        let contents = either (const "") id result
+        let comments' = makeNonVirtual comments contents
+        modifyIORef ref (\x -> comments' ++ x)
+
+finish ref = do
+    list <- readIORef ref
+    BL.putStrLn $ encode $ Json1Output { comments = list }

src/ShellCheck/Formatter/Quiet.hs

@@ -0,0 +1,36 @@
+{-
+    Copyright 2019 Austin Voecks
+
+    This file is part of ShellCheck.
+    https://www.shellcheck.net
+
+    ShellCheck is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    ShellCheck is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+-}
+module ShellCheck.Formatter.Quiet (format) where
+
+import ShellCheck.Interface
+import ShellCheck.Formatter.Format
+
+import Control.Monad
+import Data.IORef
+import System.Exit
+
+format :: FormatterOptions -> IO Formatter
+format options =
+    return Formatter {
+        header = return (),
+        footer = return (),
+        onFailure = \ _ _ -> exitFailure,
+        onResult  = \ result _ -> unless (null $ crComments result) exitFailure
+    }

src/ShellCheck/Formatter/TTY.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -19,10 +19,14 @@
 -}
 module ShellCheck.Formatter.TTY (format) where
 
+import ShellCheck.Fixer
 import ShellCheck.Interface
 import ShellCheck.Formatter.Format
 
 import Control.Monad
+import Data.Array
+import Data.Foldable
+import Data.Ord
 import Data.IORef
 import Data.List
 import Data.Maybe
@@ -34,6 +38,8 @@ wikiLink = "https://www.shellcheck.net/wiki/"
 
 -- An arbitrary Ord thing to order warnings
 type Ranking = (Char, Severity, Integer)
+-- Ansi coloring function
+type ColorFunc = (String -> String -> String)
 
 format :: FormatterOptions -> IO Formatter
 format options = do
@@ -51,6 +57,7 @@ colorForLevel level =
         "warning" -> 33 -- yellow
         "info"    -> 32 -- green
         "style"   -> 32 -- green
+        "verbose" -> 32 -- green
         "message" -> 1 -- bold
         "source"  -> 0 -- none
         _ -> 0         -- none
@@ -95,7 +102,7 @@ outputWiki errRef = do
   where
     showErr (_, code, msg) =
         putStrLn $ "  " ++ wikiLink ++ "SC" ++ show code ++ " -- " ++ shorten msg
-    limit = 40
+    limit = 36
     shorten msg =
         if length msg < limit
         then msg
@@ -116,73 +123,54 @@ outputForFile color sys comments = do
     let fileName = sourceFile (head comments)
     result <- (siReadFile sys) fileName
     let contents = either (const "") id result
-    let fileLines = lines contents
-    let lineCount = fromIntegral $ length fileLines
+    let fileLinesList = lines contents
+    let lineCount = length fileLinesList
+    let fileLines = listArray (1, lineCount) fileLinesList
     let groups = groupWith lineNo comments
     mapM_ (\commentsForLine -> do
-        let lineNum = lineNo (head commentsForLine)
+        let lineNum = fromIntegral $ lineNo (head commentsForLine)
         let line = if lineNum < 1 || lineNum > lineCount
                         then ""
-                        else fileLines !! fromIntegral (lineNum - 1)
+                        else fileLines ! fromIntegral lineNum
         putStrLn ""
         putStrLn $ color "message" $
            "In " ++ fileName ++" line " ++ show lineNum ++ ":"
         putStrLn (color "source" line)
         mapM_ (\c -> putStrLn (color (severityText c) $ cuteIndent c)) commentsForLine
         putStrLn ""
-        -- FIXME: Enable when reasonably stable
-        -- showFixedString color comments lineNum line
+        showFixedString color commentsForLine (fromIntegral lineNum) fileLines
       ) groups
 
-hasApplicableFix lineNum comment = fromMaybe False $ do
-    replacements <- fixReplacements <$> pcFix comment
-    guard $ all (\c -> onSameLine (repStartPos c) && onSameLine (repEndPos c)) replacements
-    return True
+-- Pick out only the lines necessary to show a fix in action
+sliceFile :: Fix -> Array Int String -> (Fix, Array Int String)
+sliceFile fix lines =
+    (mapPositions adjust fix, sliceLines lines)
   where
-    onSameLine pos = posLine pos == lineNum
+    (minLine, maxLine) =
+        foldl (\(mm, mx) pos -> ((min mm $ fromIntegral $ posLine pos), (max mx $ fromIntegral $ posLine pos)))
+                (maxBound, minBound) $
+            concatMap (\x -> [repStartPos x, repEndPos x]) $ fixReplacements fix
+    sliceLines :: Array Int String -> Array Int String
+    sliceLines = ixmap (1, maxLine - minLine + 1) (\x -> x + minLine - 1)
+    adjust pos =
+        pos {
+            posLine = posLine pos - (fromIntegral minLine) + 1
+        }
 
--- FIXME: Work correctly with multiple replacements
-showFixedString color comments lineNum line =
-    case filter (hasApplicableFix lineNum) comments of
-        (first:_) -> do
+showFixedString :: ColorFunc -> [PositionedComment] -> Int -> Array Int String -> IO ()
+showFixedString color comments lineNum fileLines =
+    let line = fileLines ! fromIntegral lineNum in
+    case mapMaybe pcFix comments of
+        [] -> return ()
+        fixes -> do
+            -- Folding automatically removes overlap
+            let mergedFix = fold fixes
+            -- We show the complete, associated fixes, whether or not it includes this
+            -- and/or other unrelated lines.
+            let (excerptFix, excerpt) = sliceFile mergedFix fileLines
             -- in the spirit of error prone
             putStrLn $ color "message" "Did you mean: "
-            putStrLn $ fixedString first line
-            putStrLn ""
-        _ -> return ()
-
--- need to do something smart about sorting by end index
-fixedString :: PositionedComment -> String -> String
-fixedString comment line =
-    case (pcFix comment) of
-    Nothing -> ""
-    Just rs ->
-        applyReplacement (fixReplacements rs) line 0
-        where
-            applyReplacement [] s _ = s
-            applyReplacement (rep:xs) s offset =
-                let replacementString = repString rep
-                    start = (posColumn . repStartPos) rep
-                    end = (posColumn . repEndPos) rep
-                    z = doReplace start end s replacementString
-                    len_r = (fromIntegral . length) replacementString in
-                applyReplacement xs z (offset + (end - start) + len_r)
-
--- FIXME: Work correctly with tabs
--- start and end comes from pos, which is 1 based
--- doReplace 0 0 "1234" "A" -> "A1234" -- technically not valid
--- doReplace 1 1 "1234" "A" -> "A1234"
--- doReplace 1 2 "1234" "A" -> "A234"
--- doReplace 3 3 "1234" "A" -> "12A34"
--- doReplace 4 4 "1234" "A" -> "123A4"
--- doReplace 5 5 "1234" "A" -> "1234A"
-doReplace start end o r =
-    let si = fromIntegral (start-1)
-        ei = fromIntegral (end-1)
-        (x, xs) = splitAt si o
-        (y, z) = splitAt (ei - si) xs
-    in
-    x ++ r ++ z
+            putStrLn $ unlines $ applyFix excerptFix excerpt
 
 cuteIndent :: PositionedComment -> String
 cuteIndent comment =
@@ -198,14 +186,9 @@ cuteIndent comment =
 
 code num = "SC" ++ show num
 
+getColorFunc :: ColorOption -> IO ColorFunc
 getColorFunc colorOption = do
-    term <- hIsTerminalDevice stdout
-    let windows = "mingw" `isPrefixOf` os
-    let isUsableTty = term && not windows
-    let useColor = case colorOption of
-                       ColorAlways -> True
-                       ColorNever -> False
-                       ColorAuto -> isUsableTty
+    useColor <- shouldOutputColor colorOption
     return $ if useColor then colorComment else const id
   where
     colorComment level comment =

src/ShellCheck/Interface.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -21,11 +21,11 @@
 module ShellCheck.Interface
     (
     SystemInterface(..)
-    , CheckSpec(csFilename, csScript, csCheckSourced, csExcludedWarnings, csShellTypeOverride, csMinSeverity)
+    , CheckSpec(csFilename, csScript, csCheckSourced, csIncludedWarnings, csExcludedWarnings, csShellTypeOverride, csMinSeverity, csIgnoreRC, csOptionalChecks)
     , CheckResult(crFilename, crComments)
-    , ParseSpec(psFilename, psScript, psCheckSourced, psShellTypeOverride)
+    , ParseSpec(psFilename, psScript, psCheckSourced, psIgnoreRC, psShellTypeOverride)
     , ParseResult(prComments, prTokenPositions, prRoot)
-    , AnalysisSpec(asScript, asShellType, asExecutionMode, asCheckSourced, asTokenPositions)
+    , AnalysisSpec(asScript, asShellType, asFallbackShell, asExecutionMode, asCheckSourced, asTokenPositions, asOptionalChecks)
     , AnalysisResult(arComments)
     , FormatterOptions(foColorOption, foWikiLinkCount)
     , Shell(Ksh, Sh, Bash, Dash)
@@ -46,28 +46,43 @@ module ShellCheck.Interface
     , newPosition
     , newTokenComment
     , mockedSystemInterface
+    , mockRcFile
     , newParseSpec
     , emptyCheckSpec
     , newPositionedComment
     , newComment
     , Fix(fixReplacements)
     , newFix
-    , Replacement(repStartPos, repEndPos, repString)
+    , InsertionPoint(InsertBefore, InsertAfter)
+    , Replacement(repStartPos, repEndPos, repString, repPrecedence, repInsertionPoint)
     , newReplacement
+    , CheckDescription(cdName, cdDescription, cdPositive, cdNegative)
+    , newCheckDescription
     ) where
 
 import ShellCheck.AST
 
 import Control.DeepSeq
 import Control.Monad.Identity
+import Data.List
 import Data.Monoid
+import Data.Ord
+import Data.Semigroup
 import GHC.Generics (Generic)
 import qualified Data.Map as Map
 
 
-newtype SystemInterface m = SystemInterface {
+data SystemInterface m = SystemInterface {
     -- Read a file by filename, or return an error
-    siReadFile :: String -> m (Either ErrorMessage String)
+    siReadFile :: String -> m (Either ErrorMessage String),
+    -- Given:
+    --   the current script,
+    --   a list of source-path annotations in effect,
+    --   and a sourced file,
+    --   find the sourced file
+    siFindSource :: String -> [String] -> String -> m FilePath,
+    -- Get the configuration file (name, contents) for a filename
+    siGetConfig :: String -> m (Maybe (FilePath, String))
 }
 
 -- ShellCheck input and output
@@ -75,9 +90,12 @@ data CheckSpec = CheckSpec {
     csFilename :: String,
     csScript :: String,
     csCheckSourced :: Bool,
+    csIgnoreRC :: Bool,
     csExcludedWarnings :: [Integer],
+    csIncludedWarnings :: Maybe [Integer],
     csShellTypeOverride :: Maybe Shell,
-    csMinSeverity :: Severity
+    csMinSeverity :: Severity,
+    csOptionalChecks :: [String]
 } deriving (Show, Eq)
 
 data CheckResult = CheckResult {
@@ -96,9 +114,12 @@ emptyCheckSpec = CheckSpec {
     csFilename = "",
     csScript = "",
     csCheckSourced = False,
+    csIgnoreRC = False,
     csExcludedWarnings = [],
+    csIncludedWarnings = Nothing,
     csShellTypeOverride = Nothing,
-    csMinSeverity = StyleC
+    csMinSeverity = StyleC,
+    csOptionalChecks = []
 }
 
 newParseSpec :: ParseSpec
@@ -106,6 +127,7 @@ newParseSpec = ParseSpec {
     psFilename = "",
     psScript = "",
     psCheckSourced = False,
+    psIgnoreRC = False,
     psShellTypeOverride = Nothing
 }
 
@@ -114,6 +136,7 @@ data ParseSpec = ParseSpec {
     psFilename :: String,
     psScript :: String,
     psCheckSourced :: Bool,
+    psIgnoreRC :: Bool,
     psShellTypeOverride :: Maybe Shell
 } deriving (Show, Eq)
 
@@ -134,16 +157,20 @@ newParseResult = ParseResult {
 data AnalysisSpec = AnalysisSpec {
     asScript :: Token,
     asShellType :: Maybe Shell,
+    asFallbackShell :: Maybe Shell,
     asExecutionMode :: ExecutionMode,
     asCheckSourced :: Bool,
+    asOptionalChecks :: [String],
     asTokenPositions :: Map.Map Id (Position, Position)
 }
 
 newAnalysisSpec token = AnalysisSpec {
     asScript = token,
     asShellType = Nothing,
+    asFallbackShell = Nothing,
     asExecutionMode = Executed,
     asCheckSourced = False,
+    asOptionalChecks = [],
     asTokenPositions = Map.empty
 }
 
@@ -166,6 +193,19 @@ newFormatterOptions = FormatterOptions {
     foWikiLinkCount = 3
 }
 
+data CheckDescription = CheckDescription {
+    cdName :: String,
+    cdDescription :: String,
+    cdPositive :: String,
+    cdNegative :: String
+    }
+
+newCheckDescription = CheckDescription {
+    cdName = "",
+    cdDescription = "",
+    cdPositive = "",
+    cdNegative = ""
+    }
 
 -- Supporting data types
 data Shell = Ksh | Sh | Bash | Dash deriving (Show, Eq)
@@ -180,7 +220,7 @@ data Position = Position {
     posFile :: String,    -- Filename
     posLine :: Integer,   -- 1 based source line
     posColumn :: Integer  -- 1 based source column, where tabs are 8
-} deriving (Show, Eq, Generic, NFData)
+} deriving (Show, Eq, Generic, NFData, Ord)
 
 newPosition :: Position
 newPosition = Position {
@@ -206,13 +246,25 @@ newComment = Comment {
 data Replacement = Replacement {
     repStartPos :: Position,
     repEndPos :: Position,
-    repString :: String
+    repString :: String,
+    -- Order in which the replacements should happen: highest precedence first.
+    repPrecedence :: Int,
+    -- Whether to insert immediately before or immediately after the specified region.
+    repInsertionPoint :: InsertionPoint
 } deriving (Show, Eq, Generic, NFData)
 
+data InsertionPoint = InsertBefore | InsertAfter
+    deriving (Show, Eq, Generic, NFData)
+
+instance Ord Replacement where
+    compare r1 r2 = (repStartPos r1) `compare` (repStartPos r2)
+
 newReplacement = Replacement {
     repStartPos = newPosition,
     repEndPos = newPosition,
-    repString = ""
+    repString = "",
+    repPrecedence = 1,
+    repInsertionPoint = InsertAfter
 }
 
 data Fix = Fix {
@@ -259,11 +311,18 @@ data ColorOption =
 -- For testing
 mockedSystemInterface :: [(String, String)] -> SystemInterface Identity
 mockedSystemInterface files = SystemInterface {
-    siReadFile = rf
+    siReadFile = rf,
+    siFindSource = fs,
+    siGetConfig = const $ return Nothing
 }
   where
     rf file =
         case filter ((== file) . fst) files of
             [] -> return $ Left "File not included in mock."
             [(_, contents)] -> return $ Right contents
+    fs _ _ file = return file
+
+mockRcFile rcfile mock = mock {
+    siGetConfig = const . return $ Just (".shellcheckrc", rcfile)
+}
 

src/ShellCheck/Parser.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -69,7 +69,7 @@ variableChars = upper <|> lower <|> digit <|> oneOf "_"
 functionChars = variableChars <|> oneOf ":+?-./^@"
 -- Chars to allow in functions using the 'function' keyword
 extendedFunctionChars = functionChars <|> oneOf "[]*=!"
-specialVariable = oneOf "@*#?-$!"
+specialVariable = oneOf (concat specialVariables)
 paramSubSpecialChars = oneOf "/:+-=%"
 quotableChars = "|&;<>()\\ '\t\n\r\xA0" ++ doubleQuotableChars
 quotable = almostSpace <|> oneOf quotableChars
@@ -113,6 +113,7 @@ allspacing = do
 allspacingOrFail = do
     s <- allspacing
     when (null s) $ fail "Expected whitespace"
+    return s
 
 readUnicodeQuote = do
     start <- startSpan
@@ -137,7 +138,6 @@ almostSpace =
         return ' '
 
 --------- Message/position annotation on top of user state
-data Note = Note Id Severity Code String deriving (Show, Eq)
 data ParseNote = ParseNote SourcePos SourcePos Severity Code String deriving (Show, Eq)
 data Context =
         ContextName SourcePos String
@@ -165,10 +165,6 @@ initialUserState = UserState {
 }
 
 codeForParseNote (ParseNote _ _ _ code _) = code
-noteToParseNote map (Note id severity code message) =
-        ParseNote pos pos severity code message
-    where
-        pos = fromJust $ Map.lookup id map
 
 getLastId = lastId <$> getState
 
@@ -263,6 +259,15 @@ shouldIgnoreCode code = do
     disabling' (DisableComment n) = code == n
     disabling' _ = False
 
+getCurrentAnnotations includeSource =
+    concatMap get . takeWhile (not . isBoundary) <$> getCurrentContexts
+  where
+    get (ContextAnnotation list) = list
+    get _ = []
+    isBoundary (ContextSource _) = not includeSource
+    isBoundary _ = False
+
+
 shouldFollow file = do
     context <- getCurrentContexts
     if any isThisFile context
@@ -306,6 +311,8 @@ initialSystemState = SystemState {
 data Environment m = Environment {
     systemInterface :: SystemInterface m,
     checkSourced :: Bool,
+    ignoreRC :: Bool,
+    currentFilename :: String,
     shellTypeOverride :: Maybe Shell
 }
 
@@ -949,9 +956,12 @@ prop_readAnnotation6 = isOk readAnnotation "# shellcheck disable=SC1234 # shellc
 readAnnotation = called "shellcheck directive" $ do
     try readAnnotationPrefix
     many1 linewhitespace
+    readAnnotationWithoutPrefix
+
+readAnnotationWithoutPrefix = do
     values <- many1 readKey
     optional readAnyComment
-    void linefeed <|> do
+    void linefeed <|> eof <|> do
         parseNote ErrorC 1125 "Invalid key=value pair? Ignoring the rest of this directive starting here."
         many (noneOf "\n")
         void linefeed <|> eof
@@ -960,7 +970,7 @@ readAnnotation = called "shellcheck directive" $ do
   where
     readKey = do
         keyPos <- getPosition
-        key <- many1 letter
+        key <- many1 (letter <|> char '-')
         char '=' <|> fail "Expected '=' after directive key"
         annotations <- case key of
             "disable" -> readCode `sepBy` char ','
@@ -970,10 +980,18 @@ readAnnotation = called "shellcheck directive" $ do
                     int <- many1 digit
                     return $ DisableComment (read int)
 
+            "enable" -> readName `sepBy` char ','
+              where
+                readName = EnableComment <$> many1 (letter <|> char '-')
+
             "source" -> do
                 filename <- many1 $ noneOf " \n"
                 return [SourceOverride filename]
 
+            "source-path" -> do
+                dirname <- many1 $ noneOf " \n"
+                return [SourcePath dirname]
+
             "shell" -> do
                 pos <- getPosition
                 shell <- many1 $ noneOf " \n"
@@ -1200,7 +1218,7 @@ readBackTicked quoted = called "backtick expansion" $ do
             suggestForgotClosingQuote startPos endPos "backtick expansion"
 
     -- Result positions may be off due to escapes
-    result <- subParse subStart subParser (unEscape subString)
+    result <- subParse subStart (tryWithErrors subParser <|> return []) (unEscape subString)
     return $ T_Backticked id result
   where
     unEscape [] = []
@@ -1506,10 +1524,10 @@ ensureDollar =
 
 readNormalDollar = do
     ensureDollar
-    readDollarExp <|> readDollarDoubleQuote <|> readDollarSingleQuote <|> readDollarLonely
+    readDollarExp <|> readDollarDoubleQuote <|> readDollarSingleQuote <|> readDollarLonely False
 readDoubleQuotedDollar = do
     ensureDollar
-    readDollarExp <|> readDollarLonely
+    readDollarExp <|> readDollarLonely True
 
 
 prop_readDollarExpression1 = isOk readDollarExpression "$(((1) && 3))"
@@ -1611,7 +1629,7 @@ readDollarBraced = called "parameter expansion" $ do
     word <- readDollarBracedWord
     char '}'
     id <- endSpan start
-    return $ T_DollarBraced id word
+    return $ T_DollarBraced id True word
 
 prop_readDollarExpansion1= isOk readDollarExpansion "$(echo foo; ls\n)"
 prop_readDollarExpansion2= isOk readDollarExpansion "$(  )"
@@ -1638,7 +1656,7 @@ readDollarVariable = do
     let singleCharred p = do
         value <- wrapString ((:[]) <$> p)
         id <- endSpan start
-        return $ (T_DollarBraced id value)
+        return $ (T_DollarBraced id False value)
 
     let positional = do
         value <- singleCharred digit
@@ -1651,7 +1669,7 @@ readDollarVariable = do
     let regular = do
         value <- wrapString readVariableName
         id <- endSpan start
-        return (T_DollarBraced id value) `attempting` do
+        return (T_DollarBraced id False value) `attempting` do
             lookAhead $ char '['
             parseNoteAt pos ErrorC 1087 "Use braces when expanding arrays, e.g. ${array[idx]} (or ${var}[.. to quiet)."
 
@@ -1671,12 +1689,32 @@ readVariableName = do
     rest <- many variableChars
     return (f:rest)
 
-readDollarLonely = do
+
+prop_readDollarLonely1 = isWarning readNormalWord "\"$\"var"
+prop_readDollarLonely2 = isWarning readNormalWord "\"$\"\"var\""
+prop_readDollarLonely3 = isOk readNormalWord "\"$\"$var"
+prop_readDollarLonely4 = isOk readNormalWord "\"$\"*"
+prop_readDollarLonely5 = isOk readNormalWord "$\"str\""
+readDollarLonely quoted = do
     start <- startSpan
     char '$'
     id <- endSpan start
-    n <- lookAhead (anyChar <|> (eof >> return '_'))
+    when quoted $ do
+        isHack <- quoteForEscape
+        when isHack $
+            parseProblemAtId id StyleC 1135
+                "Prefer escape over ending quote to make $ literal. Instead of \"It costs $\"5, use \"It costs \\$5\"."
     return $ T_Literal id "$"
+  where
+    quoteForEscape = option False $ try . lookAhead $ do
+        char '"'
+        -- Check for "foo $""bar"
+        optional $ char '"'
+        c <- anyVar
+        -- Don't trigger on [[ x == "$"* ]] or "$"$pattern
+        return $ c `notElem` "*$"
+    anyVar = variableStart <|> digit <|> specialVariable
+
 
 prop_readHereDoc = isOk readScript "cat << foo\nlol\ncow\nfoo"
 prop_readHereDoc2 = isNotOk readScript "cat <<- EOF\n  cow\n  EOF"
@@ -1916,8 +1954,9 @@ readNewlineList =
   where
     checkBadBreak = optional $ do
                 pos <- getPosition
-                try $ lookAhead (oneOf "|&") -- |, || or &&
-                parseProblemAt pos ErrorC 1133 "Unexpected start of line. If breaking lines, |/||/&& should be at the end of the previous one."
+                try $ lookAhead (oneOf "|&") --  See if the next thing could be |, || or &&
+                parseProblemAt pos ErrorC 1133
+                    "Unexpected start of line. If breaking lines, |/||/&& should be at the end of the previous one."
 readLineBreak = optional readNewlineList
 
 prop_readSeparator1 = isWarning readScript "a &; b"
@@ -2055,7 +2094,8 @@ readSimpleCommand = called "simple command" $ do
 
 
 readSource :: Monad m => Token -> SCParser m Token
-readSource t@(T_Redirecting _ _ (T_SimpleCommand cmdId _ (cmd:file:_))) = do
+readSource t@(T_Redirecting _ _ (T_SimpleCommand cmdId _ (cmd:file':rest'))) = do
+    let file = getFile file' rest'
     override <- getSourceOverride
     let literalFile = do
         name <- override `mplus` getLiteralString file
@@ -2071,15 +2111,21 @@ readSource t@(T_Redirecting _ _ (T_SimpleCommand cmdId _ (cmd:file:_))) = do
             proceed <- shouldFollow filename
             if not proceed
               then do
+                -- FIXME: This actually gets squashed without -a
                 parseNoteAtId (getId file) InfoC 1093
                     "This file appears to be recursively sourced. Ignoring."
                 return t
               else do
                 sys <- Mr.asks systemInterface
-                input <-
+                (input, resolvedFile) <-
                     if filename == "/dev/null" -- always allow /dev/null
-                    then return (Right "")
-                    else system $ siReadFile sys filename
+                    then return (Right "", filename)
+                    else do
+                        currentScript <- Mr.asks currentFilename
+                        paths <- mapMaybe getSourcePath <$> getCurrentAnnotations True
+                        resolved <- system $ siFindSource sys currentScript paths filename
+                        contents <- system $ siReadFile sys resolved
+                        return (contents, resolved)
                 case input of
                     Left err -> do
                         parseNoteAtId (getId file) InfoC 1091 $
@@ -2090,7 +2136,7 @@ readSource t@(T_Redirecting _ _ (T_SimpleCommand cmdId _ (cmd:file:_))) = do
                         id2 <- getNewIdFor cmdId
 
                         let included = do
-                            src <- subRead filename script
+                            src <- subRead resolvedFile script
                             return $ T_SourceCommand id1 t (T_Include id2 src)
 
                         let failed = do
@@ -2100,10 +2146,22 @@ readSource t@(T_Redirecting _ _ (T_SimpleCommand cmdId _ (cmd:file:_))) = do
 
                         included <|> failed
   where
+    getFile :: Token -> [Token] -> Token
+    getFile file (next:rest) =
+        case getLiteralString file of
+            Just "--" -> next
+            x -> file
+    getFile file _ = file
+
+    getSourcePath t =
+        case t of
+            SourcePath x -> Just x
+            _ -> Nothing
+
     subRead name script =
         withContext (ContextSource name) $
             inSeparateContext $
-                subParse (initialPos name) readScript script
+                subParse (initialPos name) (readScriptFile True) script
 readSource t = return t
 
 
@@ -2330,6 +2388,17 @@ readBraceGroup = called "brace group" $ do
     id <- endSpan start
     return $ T_BraceGroup id list
 
+prop_readBatsTest = isOk readBatsTest "@test 'can parse' {\n  true\n}"
+readBatsTest = called "bats @test" $ do
+    start <- startSpan
+    try $ string "@test"
+    spacing
+    name <- readNormalWord
+    spacing
+    test <- readBraceGroup
+    id <- endSpan start
+    return $ T_BatsTest id name test
+
 prop_readWhileClause = isOk readWhileClause "while [[ -e foo ]]; do sleep 1; done"
 readWhileClause = called "while loop" $ do
     start <- startSpan
@@ -2589,6 +2658,7 @@ readCompoundCommand = do
         readForClause,
         readSelectClause,
         readCaseClause,
+        readBatsTest,
         readFunctionDefinition
         ]
     spacing
@@ -2695,7 +2765,7 @@ readAssignmentWordExt lenient = try $ do
     variable <- readVariableName
     when lenient $
         optional (readNormalDollar >> parseNoteAt pos ErrorC
-                                1067 "For indirection, use (associative) arrays or 'read \"var$n\" <<< \"value\"'")
+                                1067 "For indirection, use arrays, declare \"var$n=value\", or (for sh) read/eval.")
     indices <- many readArrayIndex
     hasLeftSpace <- fmap (not . null) spacing
     pos <- getPosition
@@ -2714,9 +2784,10 @@ readAssignmentWordExt lenient = try $ do
         when (hasLeftSpace || hasRightSpace) $
             parseNoteAt pos ErrorC 1068 $
                 "Don't put spaces around the "
-                ++ if op == Append
-                    then "+= when appending."
-                    else "= in assignments."
+                ++ (if op == Append
+                    then "+= when appending"
+                    else "= in assignments")
+                ++ " (or quote to make it literal)."
         value <- readArray <|> readNormalWord
         spacing
         return $ T_Assignment id op variable indices value
@@ -2734,10 +2805,11 @@ readAssignmentWordExt lenient = try $ do
 
             string "=" >> return Assign
             ]
-    readEmptyLiteral = do
-        start <- startSpan
-        id <- endSpan start
-        return $ T_Literal id ""
+
+readEmptyLiteral = do
+    start <- startSpan
+    id <- endSpan start
+    return $ T_Literal id ""
 
 readArrayIndex = do
     start <- startSpan
@@ -2885,12 +2957,14 @@ prop_readShebang5 = isWarning readShebang "\n#!/bin/sh"
 prop_readShebang6 = isWarning readShebang " # Copyright \n!#/bin/bash"
 prop_readShebang7 = isNotOk readShebang "# Copyright \nfoo\n#!/bin/bash"
 readShebang = do
+    start <- startSpan
     anyShebang <|> try readMissingBang <|> withHeader
     many linewhitespace
     str <- many $ noneOf "\r\n"
+    id <- endSpan start
     optional carriageReturn
     optional linefeed
-    return str
+    return $ T_Literal id str
   where
     anyShebang = choice $ map try [
         readCorrect,
@@ -2966,22 +3040,72 @@ verifyEof = eof <|> choice [
         try (lookAhead p)
         action
 
-prop_readScript1 = isOk readScriptFile "#!/bin/bash\necho hello world\n"
-prop_readScript2 = isWarning readScriptFile "#!/bin/bash\r\necho hello world\n"
-prop_readScript3 = isWarning readScriptFile "#!/bin/bash\necho hello\xA0world"
-prop_readScript4 = isWarning readScriptFile "#!/usr/bin/perl\nfoo=("
-prop_readScript5 = isOk readScriptFile "#!/bin/bash\n#This is an empty script\n\n"
-readScriptFile = do
+
+readConfigFile :: Monad m => FilePath -> SCParser m [Annotation]
+readConfigFile filename = do
+    shouldIgnore <- Mr.asks ignoreRC
+    if shouldIgnore then return [] else read' filename
+  where
+    read' filename = do
+        sys <- Mr.asks systemInterface
+        contents <- system $ siGetConfig sys filename
+        case contents of
+            Nothing -> return []
+            Just (file, str) -> readConfig file str
+
+    readConfig filename contents = do
+        result <- lift $ runParserT readConfigKVs initialUserState filename contents
+        case result of
+            Right result ->
+                return result
+
+            Left err -> do
+                parseProblem ErrorC 1134 $ errorFor filename err
+                return []
+
+    errorFor filename err =
+        let line = "line " ++ (show . sourceLine $ errorPos err)
+            suggestion = getStringFromParsec $ errorMessages err
+        in
+            "Failed to process " ++ filename ++ ", " ++ line ++ ": "
+                ++ suggestion
+
+prop_readConfigKVs1 = isOk readConfigKVs "disable=1234"
+prop_readConfigKVs2 = isOk readConfigKVs "# Comment\ndisable=1234 # Comment\n"
+prop_readConfigKVs3 = isOk readConfigKVs ""
+prop_readConfigKVs4 = isOk readConfigKVs "\n\n\n\n\t \n"
+prop_readConfigKVs5 = isOk readConfigKVs "# shellcheck accepts annotation-like comments in rc files\ndisable=1234"
+readConfigKVs = do
+    anySpacingOrComment
+    annotations <- many (readAnnotationWithoutPrefix <* anySpacingOrComment)
+    eof
+    return $ concat annotations
+anySpacingOrComment =
+    many (void allspacingOrFail <|> void readAnyComment)
+
+prop_readScript1 = isOk readScript "#!/bin/bash\necho hello world\n"
+prop_readScript2 = isWarning readScript "#!/bin/bash\r\necho hello world\n"
+prop_readScript3 = isWarning readScript "#!/bin/bash\necho hello\xA0world"
+prop_readScript4 = isWarning readScript "#!/usr/bin/perl\nfoo=("
+prop_readScript5 = isOk readScript "#!/bin/bash\n#This is an empty script\n\n"
+readScriptFile sourced = do
     start <- startSpan
     pos <- getPosition
     optional $ do
         readUtf8Bom
         parseProblem ErrorC 1082
             "This file has a UTF-8 BOM. Remove it with: LC_CTYPE=C sed '1s/^...//' < yourscript ."
-    sb <- option "" readShebang
+    shebang <- readShebang <|> readEmptyLiteral
+    let (T_Literal _ shebangString) = shebang
     allspacing
     annotationStart <- startSpan
-    annotations <- readAnnotations
+    fileAnnotations <- readAnnotations
+    rcAnnotations <- if sourced
+                     then return []
+                     else do
+                        filename <- Mr.asks currentFilename
+                        readConfigFile filename
+    let annotations = fileAnnotations ++ rcAnnotations
     annotationId <- endSpan annotationStart
     let shellAnnotationSpecified =
             any (\x -> case x of ShellOverride {} -> True; _ -> False) annotations
@@ -2989,19 +3113,19 @@ readScriptFile = do
     let ignoreShebang = shellAnnotationSpecified || shellFlagSpecified
 
     unless ignoreShebang $
-        verifyShebang pos (getShell sb)
-    if ignoreShebang || isValidShell (getShell sb) /= Just False
+        verifyShebang pos (getShell shebangString)
+    if ignoreShebang || isValidShell (getShell shebangString) /= Just False
       then do
             commands <- withAnnotations annotations readCompoundListOrEmpty
             id <- endSpan start
             verifyEof
             let script = T_Annotation annotationId annotations $
-                            T_Script id sb commands
+                            T_Script id shebang commands
             reparseIndices script
         else do
             many anyChar
             id <- endSpan start
-            return $ T_Script id sb []
+            return $ T_Script id shebang []
 
   where
     basename s = reverse . takeWhile (/= '/') . reverse $ s
@@ -3018,7 +3142,7 @@ readScriptFile = do
         case isValidShell s of
             Just True -> return ()
             Just False -> parseProblemAt pos ErrorC 1071 "ShellCheck only supports sh/bash/dash/ksh scripts. Sorry!"
-            Nothing -> parseProblemAt pos InfoC 1008 "This shebang was unrecognized. Note that ShellCheck only handles sh/bash/dash/ksh."
+            Nothing -> parseProblemAt pos ErrorC 1008 "This shebang was unrecognized. ShellCheck only supports sh/bash/dash/ksh. Add a 'shell' directive to specify."
 
     isValidShell s =
         let good = s == "" || any (`isPrefixOf` s) goodShells
@@ -3035,6 +3159,7 @@ readScriptFile = do
         "ash",
         "dash",
         "bash",
+        "bats",
         "ksh"
         ]
     badShells = [
@@ -3050,7 +3175,7 @@ readScriptFile = do
 
     readUtf8Bom = called "Byte Order Mark" $ string "\xFEFF"
 
-readScript = readScriptFile
+readScript = readScriptFile False
 
 -- Interactively run a specific parser in ghci:
 -- debugParse readSimpleCommand "echo 'hello world'"
@@ -3085,6 +3210,8 @@ testEnvironment =
     Environment {
         systemInterface = (mockedSystemInterface []),
         checkSourced = False,
+        currentFilename = "myscript",
+        ignoreRC = False,
         shellTypeOverride = Nothing
     }
 
@@ -3260,6 +3387,8 @@ parseScript sys spec =
     env = Environment {
         systemInterface = sys,
         checkSourced = psCheckSourced spec,
+        currentFilename = psFilename spec,
+        ignoreRC = psIgnoreRC spec,
         shellTypeOverride = psShellTypeOverride spec
     }
 

src/ShellCheck/Regex.hs

@@ -1,5 +1,5 @@
 {-
-    Copyright 2012-2015 Vidar Holen
+    Copyright 2012-2019 Vidar Holen
 
     This file is part of ShellCheck.
     https://www.shellcheck.net
@@ -30,7 +30,7 @@ import Text.Regex.TDFA
 -- Precompile the regex
 mkRegex :: String -> Regex
 mkRegex str =
-    let make :: RegexMaker Regex CompOption ExecOption String => String -> Regex
+    let make :: String -> Regex
         make = makeRegex
     in
         make str

stack.yaml

@@ -2,7 +2,7 @@
 # For more information, see: https://docs.haskellstack.org/en/stable/yaml_configuration/
 
 # Specifies the GHC version and set of packages available (e.g., lts-3.5, nightly-2015-09-21, ghc-7.10.2)
-resolver: lts-8.5
+resolver: lts-13.26
 
 # Local packages, usually specified by relative directory name
 packages:

test/check_release

@@ -0,0 +1,75 @@
+#!/usr/bin/env bash
+
+failed=0
+fail() {
+  echo "$(tput setaf 1)$*$(tput sgr0)"
+  failed=1
+}
+
+if git diff | grep -q ""
+then
+  fail "There are uncommited changes"
+fi
+
+current=$(git tag --points-at)
+if [[ -z "$current" ]]
+then
+  fail "No git tag on the current commit"
+  echo "Create one with:   git tag -a v0.0.0"
+fi
+
+if [[ "$current" != v* ]]
+then
+  fail "Bad tag format: expected v0.0.0"
+fi
+
+if [[ "$(git cat-file -t "$current")" != "tag" ]]
+then
+  fail "Current tag is not annotated (required for Snap)."
+fi
+
+if [[ "$(git tag --points-at master)" != "$current" ]]
+then
+  fail "You are not on master"
+fi
+
+version=${current#v}
+if ! grep "Version:" ShellCheck.cabal | grep -qFw "$version"
+then
+  fail "The cabal file does not match tag version $version"
+fi
+
+if ! grep -qF "## $current" CHANGELOG.md
+then
+  fail "CHANGELOG.md does not contain '## $current'"
+fi
+
+if [[ $(git log -1 --pretty=%B) != "Stable version "* ]]
+then
+  fail "Expected git log message to be 'Stable version ...'"
+fi
+
+i=1 j=1
+cat << EOF
+
+Manual Checklist
+
+$((i++)). Make sure none of the automated checks above failed
+$((i++)). Make sure Travis build currently passes: https://travis-ci.org/koalaman/shellcheck
+$((i++)). Make sure SnapCraft build currently works: https://build.snapcraft.io/user/koalaman
+$((i++)). Run test/distrotest to ensure that most distros can build OOTB.
+$((i++)). Format and read over the manual for bad formatting and outdated info.
+$((i++)). Make sure the Hackage package builds, so that all files are 
+
+Release Steps
+
+$((j++)). \`cabal sdist\` to generate a Hackage package
+$((j++)). \`git push --follow-tags\` to push commit
+$((j++)). Wait for Travis to build
+$((j++)). Verify release:
+  a. Check that the new versions are uploaded: https://shellcheck.storage.googleapis.com/index.html
+  b. Check that the docker images have version tags: https://hub.docker.com/u/koalaman
+$((j++)). If no disaster, upload to Hackage: http://hackage.haskell.org/upload
+$((j++)). Push a new commit that updates CHANGELOG.md
+EOF
+exit "$failed"

test/distrotest

@@ -16,10 +16,14 @@ and is still highly experimental.
 
 Make sure you're plugged in and have screen/tmux in place,
 then re-run with $0 --run to continue.
+
+Also note that 'dist' will be deleted.
 EOF
 exit 0
 }
 
+echo "Deleting 'dist'..."
+rm -rf dist
 
 log=$(mktemp) || die "Can't create temp file"
 date >> "$log" || die "Can't write to log"
@@ -57,19 +61,20 @@ done << EOF
 debian:stable         apt-get update && apt-get install -y cabal-install
 debian:testing        apt-get update && apt-get install -y cabal-install
 ubuntu:latest         apt-get update && apt-get install -y cabal-install
-opensuse:latest       zypper install -y cabal-install ghc
+opensuse/leap:latest  zypper install -y cabal-install ghc
 
-# Older Ubuntu versions we want to support
-ubuntu:18.04          apt-get update && apt-get install -y cabal-install
-ubuntu:17.10          apt-get update && apt-get install -y cabal-install
+# Other Ubuntu versions we want to support
+ubuntu:19.04          apt-get update && apt-get install -y cabal-install
+ubuntu:18.10          apt-get update && apt-get install -y cabal-install
 
-# Misc
+# Misc Haskell including current and latest Stack build
+ubuntu:18.10          set -e; apt-get update && apt-get install -y curl && curl -sSL https://get.haskellstack.org/ | sh -s - -f && cd /mnt && exec test/stacktest
 haskell:latest        true
 
 # Known to currently fail
 centos:latest         yum install -y epel-release && yum install -y cabal-install
 fedora:latest         dnf install -y cabal-install
-base/archlinux:latest pacman -S -y --noconfirm cabal-install ghc-static base-devel
+archlinux/base:latest pacman -S -y --noconfirm cabal-install ghc-static base-devel
 EOF
 
 exit "$final"

test/shellcheck.hs

@@ -2,22 +2,28 @@ module Main where
 
 import Control.Monad
 import System.Exit
-import qualified ShellCheck.Checker
 import qualified ShellCheck.Analytics
 import qualified ShellCheck.AnalyzerLib
-import qualified ShellCheck.Parser
+import qualified ShellCheck.Checker
 import qualified ShellCheck.Checks.Commands
+import qualified ShellCheck.Checks.Custom
 import qualified ShellCheck.Checks.ShellSupport
+import qualified ShellCheck.Fixer
+import qualified ShellCheck.Formatter.Diff
+import qualified ShellCheck.Parser
 
 main = do
     putStrLn "Running ShellCheck tests..."
     results <- sequence [
-        ShellCheck.Checker.runTests,
-        ShellCheck.Checks.Commands.runTests,
-        ShellCheck.Checks.ShellSupport.runTests,
-        ShellCheck.Analytics.runTests,
-        ShellCheck.AnalyzerLib.runTests,
-        ShellCheck.Parser.runTests
+        ShellCheck.Analytics.runTests
+        ,ShellCheck.AnalyzerLib.runTests
+        ,ShellCheck.Checker.runTests
+        ,ShellCheck.Checks.Commands.runTests
+        ,ShellCheck.Checks.Custom.runTests
+        ,ShellCheck.Checks.ShellSupport.runTests
+        ,ShellCheck.Fixer.runTests
+        ,ShellCheck.Formatter.Diff.runTests
+        ,ShellCheck.Parser.runTests
       ]
     if and results
       then exitSuccess

test/stacktest

@@ -0,0 +1,27 @@
+#!/bin/bash
+# This script builds ShellCheck through `stack` using
+# various resolvers. It's run via distrotest.
+
+resolvers=(
+  nightly-"$(date -d "3 days ago" +"%Y-%m-%d")"
+)
+
+die() { echo "$*" >&2; exit 1; }
+
+[ -e "ShellCheck.cabal" ] ||
+  die "ShellCheck.cabal not in current dir"
+[ -e "stack.yaml" ] ||
+  die "stack.yaml not in current dir"
+command -v stack ||
+  die "stack is missing"
+
+stack setup        || die "Failed to setup with default resolver"
+stack build --test || die "Failed to build/test with default resolver"
+
+for resolver in "${resolvers[@]}"
+do
+  stack --resolver="$resolver" setup        || die "Failed to setup $resolver"
+  stack --resolver="$resolver" build --test || die "Failed build/test with $resolver!"
+done
+
+echo "Success"