Merge pull request #21 from hammerlab/dev

Put dev into master
lib: fix git calls Vs symbolic links

Some commands (for older git installations) do work properly with
symbolic links in the middle of the paths.
doc: fix typo in `Long-Running_Plugins.md`
doc: improve the “quick start” section
lib: implement the PBS backend + integration test

There is a new module `Ketrew_pbs` which implements LONG_RUNNING with
PBS/Torque. This was developed in conjunction with integration tests:
the test uses Ketrew to build a vagrant VM with Torque installed; then
the PBS setup is finalized, and then 2 PBS jobs are run (one of them
always fails, it is supposed to).
lib: fix bug in `Engine.add_targets`

When checking targets for redundancies Ketrew was testing only against
the targets in the database; not the ones within the request itself.
lib: factor common long-running plugins code

This creates a new module oddly named `Ketrew_long_running_utilities`
which contains things done in every long-running plugin so far.

In the process, LSF and Daemonize backends got more “precise” about
setting a target as “failed.” The previous code was sometimes setting as
failed a target even if it was technically succesful.
git: update `.gitignore` file
meta: remove links from the README
Merge pull request #22 from hammerlab/pbs_backend

Pbs backend + bug fix
Merge pull request #23 from hammerlab/long_running_factorization

lib: factor common long-running plugins code
Merge `pbs_backend` into `master` (propagate #23)
lib: add the `ps -g <pid>` query to Daemonize jobs
lib: add the `bjobs -l` query for LSF jobs
lib: add the `qstat -f1` query to PBS jobs
lib: get HTTP body in any case and fix display

Now the client always consumes the body stream replied by the server;
and hence displays more meaningful errors.
This fixes the issue #28.
lib: add `Engine.Measurements.get_all`
lib: add sub-command `inspect`

The command for now the command can only display the measurements in the
DB:

    ketrew inspect all measurements [-e]
lib: add unique i to HTTP request measurements
lib: display `http-request durations` measurement