minor correction to mwhs's answer for the windows portion...
The move command does not work for the .\features folder because... well, frankly because Windows is retarded (you can use wildcards with 'move' on files, but apparently wildcards + folders == ignore the command). Anyway, this should work as an alternative to the windows snippet provided for step #2 in his answer.
as a batch file:
@echo off
set eclipse_dir=C:\eclipse_luna
mkdir disabled
mkdir disabled\features
mkdir disabled\plugins
move plugins\org.eclipse.jpt.* disabled\plugins
for /f %%i in ('dir "%eclipse_dir%\features\org.eclipse.jpt.*" /ad /b') do (
move "%eclipse_dir%\features\%%i" "%eclipse_dir%\disabled\features\%%i"
)