Move bin/phpdoc.php to bin/phpdoc

Maintain bin/phpdoc.php for the time being but trigger an
E_USER_DEPRECATED error
Merge branch 'rename-bin-file' of https://github.com/tommygnr/phpDocumentor2 into feature/965

Conflicts:
	bin/phpdoc.php
	build.xml
	composer.json
	docs/manual/for-users/getting-started/running-the-application.rst
	docs/manual/for-users/installation/troubleshooting.rst
	features/bootstrap/ExecutionContext.php
	src/phpDocumentor/PharCompiler.php
Merge pull request #1230 from mvriel/feature/965

Change executable from phpdoc.php to phpdoc