Disable javaextdirs setting in Scala projects.

This setting is appended to the Scala class path. It defaults to the running JDK
extdirs, and that can cause trouble when the project JDK is different from the
JRE used to launch Eclipse.

Fix #1002072
Removes misc deprecated and unhygienic elements.
Merge pull request #659 from huitseeker/issue/lints

Removes misc deprecated and unhygienic elements.
Merge pull request #658 from dragos/issue/extdirs

Disable javaextdirs setting in Scala projects.