chkrootkit scan

[utu]

The following suspicious files and directories were found:

Leaving out the part that's NOT suspicious...

I've re-formatted the 'suspicious' part of your file in post #1:

root@Microknoppix:/home/knoppix# sudo chkrootkit
Searching for suspicious files and dirs, it may take a while... The following suspicious files and directories were found:  
/usr/lib/jvm/.java-1.6.0-openjdk-i386.jinfo 
/usr/lib/mono/xbuild-frameworks/.NETFramework
/usr/lib/debug/.build-id 
/usr/lib/eclipse/p2/org.eclipse.equinox.p2.engine/.settings 
/usr/lib/eclipse/p2/org.eclipse.equinox.p2.engine/profileRegistry/PlatformProfile.profile/.data 
/usr/lib/eclipse/p2/org.eclipse.equinox.p2.engine/profileRegistry/PlatformProfile.profile/.data/.settings 
/usr/lib/eclipse/p2/org.eclipse.equinox.p2.engine/profileRegistry/PlatformProfile.profile/.lock
/usr/lib/eclipse/dropins/jdt/plugins/org.eclipse.jdt.debug_3.7.1.dist/.api_description 
/usr/lib/eclipse/dropins/sdk/plugins/org.eclipse.pde.build_3.7.0.dist/.api_description 
/usr/lib/eclipse/dropins/sdk/plugins/org.eclipse.pde.build_3.7.0.dist/.options /usr/lib/eclipse/.eclipseproduct
/usr/lib/eclipse/configuration/org.eclipse.osgi/bundles/28/1/.cp 
/usr/lib/eclipse/configuration/org.eclipse.osgi/bundles/147/1/.cp 
/usr/lib/eclipse/plugins/org.eclipse.ui.intro.universal_3.2.500.dist/.api_description 
/usr/lib/eclipse/plugins/org.eclipse.ui.intro.universal_3.2.500.dist/.options 
/usr/lib/eclipse/plugins/org.eclipse.core.runtime.compatibility.registry_3.5.0.dist/.api_description 
/usr/lib/eclipse/plugins/org.eclipse.ui.workbench.compatibility_3.2.100.dist/.api_description 
/usr/lib/xulrunner-1.9.1/.autoreg /usr/lib/python2.6/dist-packages/PyQt4/uic/widget-plugins/.noinit
/usr/lib/python2.7/dist-packages/PyQt4/uic/widget-plugins/.noinit /usr/lib/pymodules/python2.6/.path 
/usr/lib/pymodules/python2.7/.path /usr/lib/icedove/.autoreg /lib/init/rw/.mdadm
/usr/lib/mono/xbuild-frameworks/.NETFramework 
/usr/lib/debug/.build-id 
/usr/lib/eclipse/p2/org.eclipse.equinox.p2.engine/.settings 
/usr/lib/eclipse/p2/org.eclipse.equinox.p2.engine/profileRegistry/PlatformProfile.profile/.data 
/usr/lib/eclipse/p2/org.eclipse.equinox.p2.engine/profileRegistry/PlatformProfile.profile/.data/.settings
/usr/lib/eclipse/configuration/org.eclipse.osgi/bundles/28/1/.cp
/usr/lib/eclipse/configuration/org.eclipse.osgi/bundles/147/1/.cp
/lib/init/rw/.mdadm

I don't know what it all means, but .NET is only part of what you've been told is suspicious.
Everything seems to be in either /usr/lib or /lib.
Start here, I guess.
a. what is eclipse, anyway.
b. what is .mdadm good for
c. etc...