Dynamo-consistency

New Feature:
- Allow sites to be selected based on lock required. This lets `gfal` sites run in a separate running queue.

Bug Fixes:
- Fix the PyPI description to not use references.
- Fix help message in `parser`
- Use exceptions when unmerged cleaning isn't working instead of exiting program
- Make list of unlisted directories

New features:
- Add ability to delete old files from arbitrary directories (when trying /store/logs at CERN)
- Test with dynamo in Jenkins container
- Add information to documentation, uses pdflatex to build now

Bug fixes:
- Move files used in Jenkins into container
- Fix some modules that weren't logging properly
- Fixed dynamo.v2 so that it works in local instance

New Feature:
- Add `check-phedex` executable to double check orphan files against protected datasets on PhEDEx

New Features:
- Can avoid deleting orphans through `--no-orphan` flag or false **DeleteOrphans** configuration parameter
- Get RAL dump working. Still needs timing on operation side.
- Allows summary table to have forced update (even when reading from cached files, for example)
- Run over **IgnoreDirectories** during consistency listing (not unmerged) so that they can still be recovered when missing. Still filtered out of orphans

Bugfixes:
- Allow previous missing files list to be empty
- Explicitly acquire lock before accessing Sqlite3 databases to avoid crashing
- Allow duplicate empty directory entries into history (don't know why FNAL gets this)
- If redirector list exists for a site, use it even if the global redirector doesn't work for that site
- A bunch of `emtpy` to `empty`, but not all of them... so that production doesn't break.

New Feature:
- `--cnf` parameter added to determine how to connect to a database using `--v1` option

Bugfixes:
- Invalid files only added to history database after redundant times missing
- The loggers from `dynamo_consistency.cms.unmerged` and the loggers instantiated with the `Lister` objects now properly write to the output files.
- Fixed a bug that prevented loading from cached trees in `main` module
- Fixed name of `dynamo_consistency.cms.filters` logger

New Features:
- Added script that can dump the inventory tree or the remote tree to disk
- Added "remote listing" method that reads file dumps done by RAL
- Site patterns can now be matched with Python regular expressions from command line
- Tests are now done for sl6 and sl7 (Python 2.6 and Python 2.7) on Jenkins node
- Add page documenting CMS-specific modules

Bugfix:
- dynamo_consistency init now fills dynamo_consistency.opts with members that may be needed to determine backend
- Fixed some of the dynamo_consistecy.cms sub-modules' docstrings
- Test consistency_config.json no longer checks for free memory (which killed some tests on small laptops)
- Fixed a bug where `dynamo_consistency.dynamo` submodules were logging twice