Segtools

* aggregation.R: fixed syntax error that caused segtools-aggregation to crash

* common.R: print.image: create the filepath's parent directory, if it
doesn't already exist
* fix bug related to: allow comment character of in mnemonics files,
and automatically add a comment to generated mnemonic files
* segtools-gmtk-parameters: fix bug related to: doesn't generate
hierarchical mnemonics when Segway subseg is used but has
cardinality 1

* allow comment character of in mnemonics files, and automatically
add a comment to generated mnemonic files
* segtools-html-report: fix some problem with os.path.samefile()
(maybe related to Python 2.7+)
* segtools-gmtk-parameters: doesn't generate hierarchical mnemonics
when Segway subseg is used but has cardinality 1
* add requirement of numpy>=1.3 (because histogram semantics change in that version)

* segtools-signal-distribution: added --order-tracks and --order-labels options
* install-script: now sets R_HOME enviroment variable which fixes some issues
* docs: fixed dead mnemonic file reference
* bugfix: removed 'new' argument to 'histrogram' for compatibility with
newer versions of numpy
* bugfix: segtools-html-report no longer crashes when the mnemonic file is
already in the place where it would be copied
* bugfix: fixed segtools-flatten unpacking error (when --filter option was
not specified)

* eliminated exclamation marks
* new autogen stuff from Sphinx to allow man page generation
* Bug fix: segtools-flatten now works when some files specify strand
information and others don't.
* Install script: now searches for R a little harder, program versions are
printed when found, and more errors are caught.
* segtools-flatten: added --filter option
* Docs: added workflow flowchart

* Plotting: No longer plots to screen. This makes plotting cleaner, less
error-prone, but slightly slower.
* Documentation: Updated to include command syntax