Added test/test_jam_env.py to check env setup

Makes sure that needed executables can be found in the path.
add test/test_jam_trim.py

Added a test script for running the trimming code on the test data. The
script compares the output files to a reference dictionary of sha1
checksums.
Make the ordering of input files consistent run-to-run
set up .gitignore
ignore .org~ files