Eclim org.eclim.command.Main exited with status 1 error - eclipse

Question

I have been using eclim for the past month and I was loving it.
Yesterday it all changed and now it doesn't work, the only things that changed on my machine are:
Sysadmin installed an encrypted partition not encroaching on any of the eclim or vim installation.
I Tried running another instance of eclipse on the same project from a different work space.
Eclim starts up, and performs basic functions, I can PingEclim etc.. but as soon as I try performing a save operation which is assumably exercising some java component it fails,
The output from starting eclim to the error is as follows:
java -jar "/home/user/dev/apps/eclipse/plugins/org.eclipse.equinox.launcher_1.1.1.R36x_v20101122_1400.jar" -debug -clean -refresh -application org.eclim.application_headless
Install location:
file:/home/user/dev/apps/eclipse/
Configuration file:
file:/home/user/dev/apps/eclipse/configuration/config.ini loaded
Configuration location:
file:/home/user/dev/apps/eclipse/configuration/
Framework located:
file:/home/user/dev/apps/eclipse/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar
Framework classpath:
file:/home/user/dev/apps/eclipse/plugins/org.eclipse.osgi_3.6.2.R36x_v20110210.jar
Debug options:
file:/home/user/dev/apps/eclipse/.options not found
Time to load bundles: 57
Starting application: 7989
2011-04-08 15:52:25,102 INFO [org.eclim.eclipse.AbstractEclimApplication] Workspace: /home/user/workspace
2011-04-08 15:52:25,103 INFO [org.eclim.eclipse.AbstractEclimApplication] Starting eclim...
Application Started: 9416
2011-04-08 15:52:26,132 INFO [org.eclim.eclipse.AbstractEclimApplication] Loading plugin org.eclim
2011-04-08 15:52:26,159 INFO [org.eclim.eclipse.AbstractEclimApplication] Loading plugin org.eclim.core
2011-04-08 15:52:26,467 INFO [org.eclim.plugin.core.CorePlugin] Loading eclim plugins...
2011-04-08 15:52:26,473 INFO [org.eclim.plugin.core.CorePlugin] Loading plugin org.eclim.maven
2011-04-08 15:52:26,475 INFO [org.eclim.plugin.core.CorePlugin] Loading plugin org.eclim.ant
2011-04-08 15:52:26,477 INFO [org.eclim.plugin.core.CorePlugin] Loading plugin org.eclim.jdt
2011-04-08 15:52:26,484 INFO [org.eclim.plugin.core.CorePlugin] Plugins loaded.
2011-04-08 15:52:26,485 INFO [org.eclim.eclipse.AbstractEclimApplication] Loaded plugin org.eclim.core
2011-04-08 15:52:26,489 INFO [org.eclim.eclipse.AbstractEclimApplication] Eclim Server Started on port 9091.
2011-04-08 15:52:26,580 WARN [org.eclim.plugin.jdt.PluginResources] Unable to locate jre src.zip for JAVA_HOME: /usr/lib/jvm/java-6-sun-1.6.0.24/jre
NGSession 1: 127.0.0.1: org.eclim.command.Main exited with status 1
NGSession 2: 127.0.0.1: org.eclim.command.Main exited with status 1
NGSession 1: 127.0.0.1: org.eclim.command.Main exited with status 1
With the error part beign:
NGSession 1: 127.0.0.1: org.eclim.command.Main exited with status 1
NGSession 2: 127.0.0.1: org.eclim.command.Main exited with status 1
NGSession 1: 127.0.0.1: org.eclim.command.Main exited with status 1
I have tried re-installing eclim and have tried it on a differentnew version of eclipse.
If someone could give me a clue about what is going on or point me in the direction of how I might debug then it would help.

Answer 1

I had the exact same error, which was caused by the .project folder in my code folder. I got on track of this after reading this post. After deleting the .project folder, eclimd started up just fine.
When using emacs with eclim, the *Messages*-buffer can give you hints as to what could be wrong with the process, if the problem arises after eclimd has started. In vim it should be :Messages, although I'm not sure about this as I am no vim user.