Tell Git to ignore Java build outputs and vim .swp files

Do not ignore .jar in the lib/ directory.
Import MOCHA 1.0.00.003

Download source as of 2012-08-22 15:20 from the VA FOIA site:

 https://downloads.va.gov/files/FOIA/Software/Patches_By_Application/MOCHA/sgn_PHARMO_SWRI_Code_Drop.zip

Run shell code to extract the source code of MOCHA:

 sha1=60ae038d980ad89106e62aae97ed901578ee70fb &&
 sha1sum sgn_PHARMO_SWRI_Code_Drop.zip | grep -q $sha1 &&
 unzip sgn_PHARMO_SWRI_Code_Drop.zip &&
 mv "sgn_PHARMO_SWRI_Code_Drop/vobs/PHARM0_SwRI_code_drop/MOCHA version 1.0.00.003/MOCHA_v1.0.00.003-sourcecode.zip" . &&
 rm -rf sgn_PHARMO_SWRI_Code_Drop.zip sgn_PHARMO_SWRI_Code_Drop &&
 sha1=3495edfb2deb07475dead3b485a54993ecfa35c4 &&
 sha1sum MOCHA_v1.0.00.003-sourcecode.zip | grep -q $sha1 &&
 unzip MOCHA_v1.0.00.003-sourcecode.zip &&
 (cd MOCHA_v1.0.00.003-sourcecode/PepsLite; tar c *) | tar x &&
 rm -rf MOCHA_v1.0.00.003-sourcecode.zip MOCHA_v1.0.00.003-sourcecode

Also fix permissions and line endings:

 find * -type f -print0 | xargs -0 chmod u+w &&
 find * -type f -print0 | egrep -vzZ '\.(doc|jar|png|zip|ZIP)' | xargs -0 -n 1 fromdos