Clean module.xml files

1) While removing the deprecated javax.api module a comment has been left to inform about the fact:

<!--WFLY-14219 Remove deprecated <module name="javax.api"/> -->

This can be removed, multiple versions released informed about it.

2) Some module.xml are correct files including a LF at the end, some not.
Background: https://stackoverflow.com/a/729795

Fix: Add LF where missing.