Replace gnuplot scripts with gnuplot-py usage.

System calls are not particularly portable. In particular putting
gnuplot in the path of a Windows system might take work. There's still
the upload script that assumes POSIX-ness, for want of rrdpython support
for dumping to XML, but this is a start.
Avoid copying list in CDF.
Move makeHistogram() into gnuplots module.

Also fixes bug with reject percentage tuple modification.
Move constants specific to upgrade into that scope.

They are not appropriate to have at module scope - no longer applicable
to current database versions.
Move database init and querying into class.

It seems cleaner separation to have other parts tend to work with the
database on a conceptual level - though probe.py still has direct
control over inserts. At least database things aren't spread quite so
widely throughout the codebase.
Merge branch 'module-refactor'
Update readme; todo.
Output files to output directory.

All generated files are put into the output directory. This allows
inserting an entire directory instead of specifying files individually.
Setting persistance to reboot uses a manifest putter
(DefaultManifestPutter) which is preferable for anything that doesn't
absolutely have to be inserted accross reboots. The existing manifest
putter was exhibiting nonresponsiveness in testing.
Remove default filenames from gnuplots module.

They should be specified elsewhere. To make an appropriate default now
would require knowledge of the output directory, which seems like an
unneccesary dependency.
Merge branch 'output-dir'
Fix typos.
Update TODOs.
Update changelog.