Save values (cli options) passed manually and merge with defaults

We need to save manually passed values in order to prevent using default values in `PHP_CodeSniffer::process` (`$cliValues = $this->cli->getCommandLineValues()`)

I'm not sure if this is acceptable, so I made simple changes in previous PR (https://github.com/squizlabs/PHP_CodeSniffer/pull/172). Choose which one better reflects your vision of doing this.
Updated changelog
Merge branch 'patch-2' of https://github.com/radioheaded/PHP_CodeSniffer
Changelog + coding standards
Fixed bug #20131 : PHP errors in svnblame report, if there are files not under version control
Fixed bug #20119 : PHP warning: invalid argument to str_repeat() in SVN blame report with -s
Fixed bug #20133 : Allow HG: hg_id as value for @version tag
Prepare for 1.4.8 release
Merge branch 'master' into report-memory-improvements

Conflicts:
	CodeSniffer/Reports/VersionControl.php
	package.xml
The doc generator expects an array of sniffs to limit to, not files.
Package version was not replaced here
Doc generation is now working again for installed standards