Added support for exclude patterns from pmd.

Added support for ignoring files via the exclude-pattern element in a
ruleset.
Fixed file name handling in RuleSetFactory::getIgnorePattern, updated tests
Removed use of short array syntax.
Merge branch 'master' of https://github.com/ptlis/phpmd into GH100-ptlis-exclude-pattern
Refs #100 #117: Prepared for 2.0
Merge branch 'GH100-ptlis-exclude-pattern'