Move bin/phpdoc.php to bin/phpdoc

Maintain bin/phpdoc.php for the time being but trigger an
E_USER_DEPRECATED error
Fixes #1197
Merge pull request #1220 from siad007/patch-10

Fixed #1197
Added more info

Fixes #1121
Merge pull request #1222 from siad007/patch-10

Added more info
Update MarkerFromTagsExtractor.php

Related to #1225
missed bracket
Update composer lock file
Merge branch 'develop' of github.com:phpDocumentor/phpDocumentor2 into develop
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 #1226 from siad007/patch-11

Update MarkerFromTagsExtractor.php
Fixes #1229: @method tag in a trait causes Exception

In the TraitDescriptor we assembled a MethodDescriptor when an `@method`
tag is used. But instead of reading the Method Name we tried to get a
property name from the `@method` tag definition.

Because this method is not present an exception was generated. This
commit fixes the issue by using the correct method to get the method
name.
Merge pull request #1231 from mvriel/feature/1229

Fixes #1229: @method tag in a trait causes Exception
Merge pull request #1230 from mvriel/feature/965

Change executable from phpdoc.php to phpdoc
Add test for Behaviour\Collection
Add test for Behaviour\BehaviourAbstract
prevent dropping comments for Zend Optimizer+
Merge pull request #1236 from siad007/patch-12

prevent dropping comments for Zend Optimizer+
Merge pull request #1235 from mvriel/feature/tests-for-transformer-behaviours

Looks good...
Add tests for Template-related classes