Move bin/phpdoc.php to bin/phpdoc

Maintain bin/phpdoc.php for the time being but trigger an
E_USER_DEPRECATED error
Update MarkerFromTagsExtractor.php

Related to #1225
missed bracket
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
Merge pull request #1238 from mvriel/feature/tests-for-transformer-templates

Looks good...
Better OPcache handling

Tested also under windows and fixes #1073 - for Zend Optimizer+ there is no option left than throw an exception because zend_optimizerplus.save_comments and zend_optimizerplus.enable are PHP_INI_SYSTEM settings.
Add tests for Router-related classes
Merge pull request #1240 from siad007/patch-14

Better OPcache handling
Fixes #1193: Package tags don't inherit to classes

@bskendig reported that a class without package tag did
not fall into the package that was set on the file in which
it was contained.

After research it appeared that although interfaces and traits
correctly inherited the package tag that classes tried to use the
`setPackage` method instead of the tags collection.

The setPackage method is 'reserved' to set the Package descriptor
on a descriptor and by not setting the 'package' element in the
tags collection are other parts of the application not aware that
the class falls within a specific package.

(for the interested reader: the package descriptor is set in a
compiler pass based on the package element in the tags collection)
#157: Classes do not inherit trait methods and props

Methods and properties from traits are currently not shown in the method
and property listing for a class. In this commit we treat traits equal to
parent classes and inherit their methods.