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Fixed language around phpcs:ignore annotation (issues #3657)
Fixed broken links
Updated Advanced Usage (markdown)
Updated default encoding
Add docs for comment syntax notes
Documented selective disable/enable using the new comment syntax
Changed docs to use new @codingStandards comment syntax
Removed docs about checking files with no extension (removed in 3.0)
Added extra docs about escape dot characters (ref #1592)
Documented that --runtime-set doesnt work with all config options
Added docs for @codingStandardsIgnoreLine comment
Added docs for the -q command line argument
Added docs for the --exclude CLI arg
Updated section about the phpcs.xml default configuration file
Added bootstrap option
Added TOC
Added a note to --tab-width about the DisallowTabIndentSniff ignore it
Added note about regular expression support in ignore patterns
Added docs for --runtime-set