I've got an ES2.5 turnkey installation on Windows 64bit JBoss - it was giving an error when I ran configuration Manager. I'm recording it here for future reference if other people get this error also
On Step one (Configure EAR files), was always giving the error "ALC-LCM-000-000" could not clean working directory
Livecycle was previously installed (and runs OK), but re-running Config Manager always gave this error.
To get around this, I found that once I stopped JBoss, and restarted Configuration Manager without JBoss running, I was able to Configure the EARs without this problem
The Config Manager log always recorded the stack trace error below:
[2011-07-22 10:32:15,135], SEVERE, Thread-5, com.adobe.livecycle.lcm.feature.configureLC.MergeEars2, Could not clean working directory
com.adobe.livecycle.lcm.core.LCMException[ALC-LCM-000-000]: Could not clean working directory
Caused by: java.io.IOException: Unable to delete directory ..\working\configureLC\mergeTmp\tmp.
... 9 more
Are you still facing this issue?
Did you run LCM with the same user who installed it?
Also, could you confirm that an anti-virus isn't running on your system with on-access scan enabled that might be preventing the LCM to delete this file?