Ignoring accidental .class files occuring outside of target
The undeployer produces better error messages + allows MockMascotUndeployer to be selected.
(cherry picked from commit 716bae0e90f67c0c3686f32a0b7a3eb4db7bff74)
Fixing Scaffold undeployer to support Scaffold3.
(cherry picked from commit 18482fea2e7d0a7242597eed2a96af793d9d2044)
Making sure the FASTA is properly checked for accession number and description lengths and characters.
Cleaning up AbstractRunner and SimpleRunner.
Cleaning up GridWorkPacket
Fixing the mascot tests.
Cleaning up the file token handling code.
The logs are transferred twice - at the beginning of running a task, and after everything succeeds/fails. This way a remote machine will update the logs if these are not directly accessible.
Fixing a test.
Cleaning up environment variable access.
Reducing the surface of the filesharing package.
The RMI messaging code has to go/be changed - will not work in firewalled environment.
Missed one deprecation.
The grid configuration gets saved correctly.
The default values are transmitted properly from the UI to the model.
Adding dump folder configuration to the daemon config.
Cleaning up critical FogBugz errors.
Simplifying FileHolder.
The MgfCleanup handles the SCANS header from PD.
BugsId: 1730
MgfIonsModeller warns too much about nothing.
Fixing NPE in GridWorkPacket.