handle incorrect report template much more nicely than a giant stack
trace
fix R code failing when last line contains certain syntax
slightly better description of command for specifying report template
Merge branch 'master' of https://code.google.com/p/bpipe

Conflicts:
	src/main/groovy/bpipe/Pipeline.groovy
fix command configuration sometimes not displaying name
allow command line region to override chr() within pipeline
fix merge snafu on report template name
better file names when output extension occurs in combination with
introduction of branch name (foo.chr1.csv instead of foo.txt.chr1.csv)
allow to override chr() with region from command line
bugfix - don't explode if attempting to indent a null value
silly file mody changes to may cygwin happy
Merge branch 'master' of https://code.google.com/p/bpipe
an output that is specified as an absolute / relative file that exists, fix not seeing it in dependency graph
fix msg writing output during probes
support for arbitrary list for parallelization (experimental)
added test for param override
Merge branch 'master' of https://code.google.com/p/bpipe
fix test missing -L flag
Fix output sometimes not fully flushed when running pipelines using resource managers
fix outut not fully flushed by resource managers
added ability to set branch level variables that are carried forward
through the pipeline
fix compile fail