initial changes for trace file upload
Add public/trace_files to .gitignore.
Add Colony::Observer.
Add changes for directory param.
Add observer.
Rename field as trace_file.
Tidy.
add first version of shell scripts
Add trim_blobs gem to remove logging of trace_file.
Initial changes for trace_file processing.
Tidy.
Enable Colony::Observer.
Merge branch 'crispr_dev' into crispr_dev_trace_file

Conflicts:
	app/models/colony.rb
Move code from scf.rake task to colony.rb
Change to run on t87-dev; supply params to perl script from crispr table.
remove logging
Rename remove routine.
Tidy; add new column to html table to show files generated
Add files to keep.
Tidy.