Adds BARCODES_DIR parameter to IlluminaBasecallsToFastq and
IlluminaBasecallsToSam so that they can use the barcode files from
ExtractIlluminaBarcodes when it has been run with OUTPUT_DIR different
from the BASECALLS_DIR parameter.

The use case is that the BASECALLS_DIR directory is read-only and the
barcode files can't be written to that directory and the other tools are
useless if they can't read the barcode files from a different directory.
Avoid logging a NullPointerException if IlluminaBasecallsToFastq is
started with FORCE_GC=false.

GC timer write to the 'log' instead of directly to System.out. There is
really no reason to handle this information differently than other
logging.
Update AbstractInputParser.java

Included nested exception.
File faker bug fixes.
- `ClocsFileFaker` emits too many bytes in single-record file.
- `PerTilePerCycleFileUtil` wasn't careful about cycle collisions.
Add build date to metrics definitions.
Check root html files in to github.
Reference proper source repos on the picard homepage.
Separate javadoc for picard and htsjdk.
Update release script to upload html.
Merge pull request #19 from broadinstitute/jc_update_sourceforge_website

Add build date to metrics definitions.
Create inc directory for html generated sources.
Website grammar.
Merge pull request #18 from broadinstitute/mm_bugfix_file_fakers

File faker bug fixes.
Add html upload to the build not just shtml.
Merge remote-tracking branch 'origin/master'
Merge pull request #15 from nnordborg/barcodes-dir

Add BARCODES_DIR parameter to IlluminaBasecallsToFastq and IlluminaBasecallsToSam
Merge pull request #14 from nnordborg/gc-timer-npe

FORCE_GC=false causes NPE in log
Clarify what a "non-PF read" is.
Merge pull request #17 from marcelm/master

Clarify what a "non-PF read" is.