Bpipe Version 0.9.9.9

Summary

This release includes a number of smaller features and improvements and some important fixes.

Ability to filter gitlab issues identified by title search for updating
Feature: support for 'debug' command that launches groovy shell. Add debug() to pipeline stage to launch interactive shell.
Revamp monitoring of command status for PBS/Torque based pipelines, by pooling calls to qstat between commands.
Feature: archive command to clean up .bpipe directory into restorable zip file
Support referencing params set on command line in bpipe.config
Bpipe pipelines can now accept the first line as a "shebang" so that bpipe pipelines become executable scripts. ie: make the first line of your pipeline: #!/path/to/bpipe

Fix not completely robust reading of exit code for local commands (sometimes command succeeds when shouldn't)
Fix local commands not always terminating on explicit stop
Add setsid by default to local jobs on linux - prevents some cases where jobs abort when precessing ctrl-c after starting bpipe
Fix new gitlab issues with large content failing to send
Fix possible runaway killing of processes when local preallocated jobs are explicitly stopped with bpipe stop
Fix file notifications not always incrementing and therefore overwriting previous notification
Fix notification manager not respecting timeout to allow for setup of channels
Fix possible error due to race condition reading read PID with local command executor
Fix file handle leak on some file systems with large scale highly parallelised, long running pipelines
Fix the default file notification channel overwriting files from other send channels
Fix possible error if input is referenced in details of send