Merge pull request #991 from mvriel/989

[#989]: Update monolog requirement to 1.6
Add shebang for Phar file to enable +x
Fix absence of FileDescriptor checking
Cleaned up unused code
[#985]: Fix missing namespaces and classes folder and contents
[#985]: fix erroneous paths
Update CHANGELOG for recent changes
Update dependencies to pull in a new template version
Merge branch 'master' of github.com:phpDocumentor/phpDocumentor2
Merge branch 'master' into develop

Conflicts:
	CHANGELOG.md
	composer.lock