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
Merge branch 'report-memory-improvements' into phpcs-fixer

Conflicts:
	CodeSniffer/CLI.php
	CodeSniffer/Reports/VersionControl.php
	package.xml