Use RMG.databasesDirectory system property to store where the DBs are.

This will allow us to move them.
1,3-hexadiene example now has RMG.sh bash script.

This is used in the "make test" target.
It will allow us to demonstrate and test environment variable settings.
Added RMG_DATABASES environment variable.

Default is $RMG/databases.
This is where to look for databases.
Added RMG_JOB_SCRATCH and RMG_JOB_OUTPUT environment variables.

These should both be unique to the current job (hence the JOB in the name)
and the OUTPUT should be stuff you want to keep, and the SCRATCH should
be stuff you don't mind losing but in a place that has fast I/O.

Default for both is the current working directory.
Run InChI in the RMG_JOB_SCRATCH/InChI directory.

Default behaviour should be the same as before, because
RMG_JOB_SCRATCH defaults to $PWD if it is not defined.

However, if you DO set RMG_JOB_SCRATCH then you can put it
on a faster drive, and keep your temporary InChI files out
of the way of your results.
Tweaks to path settings.

Trying to make it more robust when you have empty strings etc.
Troublesome FAME output saved to fameOutputDir

The fame input is no longer saved by default, only if it fails.
PopulateReactions example now MSC for pdep, and PopulateReactions exits when done.
Save troublesome Frankie input/output in RMG.frankieOutputDir

This should default to the same place as before: ./frankie
But will allow you to move it. 
Fix misleading typo in Frankie log message
 Fixed bug where dummy Thermo from failed QMTP was saved in qmLibrary
Changed QMTP so that failed pm3 attempts are not repeated

Conflicts:
	source/RMG/jing/chem/QMTP.java

Resolved by Richard West <r.west@neu.edu>
Removing some redundant commented code.
QMTP .hold file changes.

We now delete the hold files on exiting RMG, so that you don't end up
freezing a subsequent run waiting for ever for a something to finish a
job that's not running.

We clear the hold on the first success, and on the last failure.

Closes #277
Merge branch 'master' into paths
Refactoring the path setting stuff.

Trying to reduce duplication and improve logic.
Check MOPAC_LICENSE environment variable is correctly set, if needed.
Save 2Dmolfiles and 3Dmolfiles in $RMG_JOB_SCRATCH directory.

These are left until the end of the current job run, but the current behaviour
is to delete them, so they can't be that important (perhaps useful for debugging).
I therefore decided they belong in the scratch directory.
QMLibrary files are now opened, written, and closed for each species.

This should allow multiple concurrent runs of RMG to write to the same
QM thermo library. (They won't read from each other's results until they are 
restarted, but at least their results will all be saved in one place).
This could lead to the same species showing up several times in the list, but 
this shouldn't be a problem.
QMThermoLibrary now saved in RMG_QM_LIBRARY (new environment variable).

This allows all your jobs to use the same QM Thermo Library.
(NB. they only read it once at the start, so concurrent jobs may still
repeat QM calculations unnecessarily - unless they also share their
QM calculations Folder... coming soon!)