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Update URLs to point to the PHPCSStandards repo
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wiki/Advanced-Usage.md

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$ phpcs --tab-width=4 /path/to/code
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> Note: The [included sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/WhiteSpace/DisallowTabIndentSniff.php) that enforces space indentation will still generate errors even if you have replaced tabs with spaces using the `--tab-width` setting. This sniff looks at the unmodified version of the code to check line indentation and so must be disabled in a [[custom ruleset.xml file|Annotated ruleset]] if you want to use tab indentation.
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> Note: The [included sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/WhiteSpace/DisallowTabIndentSniff.php) that enforces space indentation will still generate errors even if you have replaced tabs with spaces using the `--tab-width` setting. This sniff looks at the unmodified version of the code to check line indentation and so must be disabled in a [[custom ruleset.xml file|Annotated ruleset]] if you want to use tab indentation.
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## Specifying an Encoding
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By default, PHP_CodeSniffer will treat all source files as if they use UTF-8 encoding. If you need your source files to be processed using a specific encoding, you can specify the encoding using the `--encoding` command line argument.
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The `phpcs.xml` file has exactly the same format as a normal [[ruleset.xml file|Annotated ruleset]], so all the same options are available in it. The `phpcs.xml` file essentially acts as a default coding standard and configuration file for a code base, and is typically used to allow the `phpcs` command to be run on a repository without specifying any arguments.
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> An example `phpcs.xml` file can be found in the PHP_CodeSniffer repository: [phpcs.xml.dist](https://raw.githubusercontent.com/squizlabs/PHP_CodeSniffer/master/phpcs.xml.dist)
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> An example `phpcs.xml` file can be found in the PHP_CodeSniffer repository: [phpcs.xml.dist](https://raw.githubusercontent.com/PHPCSStandards/PHP_CodeSniffer/master/phpcs.xml.dist)
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## Specifying php.ini Settings
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PHP_CodeSniffer allows you to set temporary php.ini settings during a run using the `-d` command line argument. The name of the php.ini setting must be specified on the command line, but the value is optional. If no value is set, the php.ini setting will be given a value of TRUE.

wiki/Coding-Standard-Tutorial.md

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* @category PHP
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* @package PHP_CodeSniffer
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* @author Your Name <you@domain.net>
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* @license https://github.com/squizlabs/PHP_CodeSniffer/blob/master/licence.txt BSD Licence
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* @link http://pear.php.net/package/PHP_CodeSniffer
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* @license https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/licence.txt BSD Licence
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*/
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namespace PHP_CodeSniffer\Standards\MyStandard\Sniffs\Commenting;

wiki/Configuration-Options.md

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## Generic Coding Standard Configuration Options
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### Setting the path to CSSLint
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The Generic coding standard [includes a sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/Debug/CSSLintSniff.php) that will check each CSS file using [CSS Lint](http://csslint.net/). Use the `csslint_path` configuration option to tell the CSSLint sniff where to find the tool.
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The Generic coding standard [includes a sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/Debug/CSSLintSniff.php) that will check each CSS file using [CSS Lint](http://csslint.net/). Use the `csslint_path` configuration option to tell the CSSLint sniff where to find the tool.
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$ phpcs --config-set csslint_path /path/to/csslint
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### Setting the path to the Google Closure Linter
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The Generic coding standard [includes a sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/Debug/ClosureLinterSniff.php) that will check each file using the [Google Closure Linter](https://github.com/google/closure-linter), an open source JavaScript style checker from Google. Use the `gjslint_path` configuration option to tell the Google Closure Linter sniff where to find the tool.
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The Generic coding standard [includes a sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/Debug/ClosureLinterSniff.php) that will check each file using the [Google Closure Linter](https://github.com/google/closure-linter), an open source JavaScript style checker from Google. Use the `gjslint_path` configuration option to tell the Google Closure Linter sniff where to find the tool.
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$ phpcs --config-set gjslint_path /path/to/gjslint
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### Setting the path to PHP
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The Generic coding standard [includes a sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/PHP/SyntaxSniff.php) that will check the syntax of each PHP file using [the built-in PHP linter](http://php.net/manual/en/features.commandline.options.php). Use the `php_path` configuration option to tell the Syntax sniff where to find the PHP binary.
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The Generic coding standard [includes a sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/PHP/SyntaxSniff.php) that will check the syntax of each PHP file using [the built-in PHP linter](http://php.net/manual/en/features.commandline.options.php). Use the `php_path` configuration option to tell the Syntax sniff where to find the PHP binary.
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$ phpcs --config-set php_path /path/to/php
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### Setting the path to JSHint
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The Generic coding standard [includes a sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/Debug/JSHintSniff.php) that will check each JavaScript file using [JSHint](http://www.jshint.com/), a tool to detect errors and potential problems in JavaScript code. Use the `jshint_path` configuration option to tell the JSHint sniff where to find the tool.
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The Generic coding standard [includes a sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Generic/Sniffs/Debug/JSHintSniff.php) that will check each JavaScript file using [JSHint](http://www.jshint.com/), a tool to detect errors and potential problems in JavaScript code. Use the `jshint_path` configuration option to tell the JSHint sniff where to find the tool.
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$ phpcs --config-set jshint_path /path/to/jshint.js
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## Squiz Coding Standard Configuration Options
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### Setting the path to JSLint
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The Squiz coding standard [includes a sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Squiz/Sniffs/Debug/JSLintSniff.php) that will check each JavaScript file using [JSLint](http://www.jslint.com/), a JavaScript program that looks for problems in JavaScript programs. Use the `jslint_path` configuration option to tell the JSLint sniff where to find the tool.
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The Squiz coding standard [includes a sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Squiz/Sniffs/Debug/JSLintSniff.php) that will check each JavaScript file using [JSLint](http://www.jslint.com/), a JavaScript program that looks for problems in JavaScript programs. Use the `jslint_path` configuration option to tell the JSLint sniff where to find the tool.
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$ phpcs --config-set jslint_path /path/to/jslint.js
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$ phpcs --config-set rhino_path /path/to/rhino
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### Setting the path to JavaScript Lint
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The Squiz coding standard [includes a sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Squiz/Sniffs/Debug/JavaScriptLintSniff.php) that will check each JavaScript file using [JavaScript Lint](http://www.javascriptlint.com/), a tool that checks all your JavaScript source code for common mistakes without actually running the script or opening the web page. Use the `jsl_path` configuration option to tell the JavaScript Lint sniff where to find the tool.
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The Squiz coding standard [includes a sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Squiz/Sniffs/Debug/JavaScriptLintSniff.php) that will check each JavaScript file using [JavaScript Lint](http://www.javascriptlint.com/), a tool that checks all your JavaScript source code for common mistakes without actually running the script or opening the web page. Use the `jsl_path` configuration option to tell the JavaScript Lint sniff where to find the tool.
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$ phpcs --config-set jsl_path /path/to/jsl
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## Zend Coding Standard Configuration Options
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### Setting the path to the Zend Code Analyzer
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The Zend coding standard [includes a sniff](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Standards/Zend/Sniffs/Debug/CodeAnalyzerSniff.php) that will check each file using the Zend Code Analyzer, a tool that comes with Zend Studio. Use the `zend_ca_path` configuration option to tell the Zend Code Analyzer sniff where to find the tool.
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The Zend coding standard [includes a sniff](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Standards/Zend/Sniffs/Debug/CodeAnalyzerSniff.php) that will check each file using the Zend Code Analyzer, a tool that comes with Zend Studio. Use the `zend_ca_path` configuration option to tell the Zend Code Analyzer sniff where to find the tool.
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$ phpcs --config-set zend_ca_path /path/to/ZendCodeAnalyzer

wiki/Fixing-Errors-Automatically.md

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PHP_CodeSniffer is able to fix many errors and warnings automatically. The `diff` report can be used to generate a diff that can be applied using the `patch` command. Alternatively, the PHP Code Beautifier and Fixer (`phpcbf`) can be used in place of `phpcs` to automatically generate and apply the diff for you.
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Screen-based reports, such as the [full](https://github.com/squizlabs/PHP_CodeSniffer/wiki/Reporting#printing-full-and-summary-reports), [summary](https://github.com/squizlabs/PHP_CodeSniffer/wiki/Reporting#printing-full-and-summary-reports) and [source](https://github.com/squizlabs/PHP_CodeSniffer/wiki/Reporting#printing-a-source-report) reports, provide information about how many errors and warnings are found. If any of the issues can be fixed automatically by `phpcbf`, additional information will be printed:
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Screen-based reports, such as the [full](https://github.com/PHPCSStandards/PHP_CodeSniffer/wiki/Reporting#printing-full-and-summary-reports), [summary](https://github.com/PHPCSStandards/PHP_CodeSniffer/wiki/Reporting#printing-full-and-summary-reports) and [source](https://github.com/PHPCSStandards/PHP_CodeSniffer/wiki/Reporting#printing-a-source-report) reports, provide information about how many errors and warnings are found. If any of the issues can be fixed automatically by `phpcbf`, additional information will be printed:
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wiki/Usage.md

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> The `--standard` command line argument is optional, even if you have more than one coding standard installed. If no coding standard is specified, PHP_CodeSniffer will default to checking against the _PEAR_ coding standard, or the standard you have set as the default. [View instructions for setting the default coding standard](https://github.com/squizlabs/PHP_CodeSniffer/wiki/Configuration-Options#setting-the-default-coding-standard).
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> The `--standard` command line argument is optional, even if you have more than one coding standard installed. If no coding standard is specified, PHP_CodeSniffer will default to checking against the _PEAR_ coding standard, or the standard you have set as the default. [View instructions for setting the default coding standard](https://github.com/PHPCSStandards/PHP_CodeSniffer/wiki/Configuration-Options#setting-the-default-coding-standard).
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## Checking Files and Folders
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* `S` : The file contained a [@codingStandardsIgnoreFile](https://github.com/squizlabs/PHP_CodeSniffer/wiki/Advanced-Usage#ignoring-files-and-folders) comment and was skipped
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* `S` : The file contained a [@codingStandardsIgnoreFile](https://github.com/PHPCSStandards/PHP_CodeSniffer/wiki/Advanced-Usage#ignoring-files-and-folders) comment and was skipped
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Progress output will look like this:
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.E.EE.E.E..E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E..E..E..E.E.E..E 540 / 572
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.E.E....E.E.E...E.....E.E.ES....
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> You can configure PHP_CodeSniffer to show progress information by default using [the configuration option](https://github.com/squizlabs/PHP_CodeSniffer/wiki/Configuration-Options#showing-progress-by-default)</link>.
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> You can configure PHP_CodeSniffer to show progress information by default using [the configuration option](https://github.com/PHPCSStandards/PHP_CodeSniffer/wiki/Configuration-Options#showing-progress-by-default)</link>.
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With verbose output enabled, PHP_CodeSniffer will print the file that it is checking, show you how many tokens and lines the file contains, and let you know how long it took to process. The output will look like this:
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wiki/Version-3.0-Upgrade-Guide.md

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> Note: A complete list of configuration settings can be found in the documentation of the [Config class](https://github.com/squizlabs/PHP_CodeSniffer/blob/master/src/Config.php#L42).
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> Note: A complete list of configuration settings can be found in the documentation of the [Config class](https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/src/Config.php#L42).
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## Upgrading Custom Reports
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