Restore 'coverage' config file

This is for testing code coverage of the unit tests using
Ned Batchelder's Coverage.py
See http://nedbatchelder.com/code/coverage/

It was added in
39080f727e35b036b1992934df1c444758e9cc7a
and accidentally removed in
d88d5a54b034d149f318100565f55aceb8e503f9
Updated .gitignore file
Add and modify calls for generateTransportData()

- move call for seed species from initialize() to
addSeedMechanismToCore()
- call getTransportData() for reactions found in reaction libraries in
addReactionLibraryToEdge()
Add function updateLonePairs() and call in fromRDKitMol()

- setting the number of lone electron pairs
- also fixes fromSMILES and similar functions using fromRDKitMol()
Merge pull request #167 from bbuesser/master

Add and modify calls for generateTransportData() and add updateLonePairs to fix adjacency lists generated by fromSMILES
Add label removeLonePairs to toAdjacencyList()

- enables printing adjacency lists without the number of lone electron
pairs per atom
- helpfulr for RMG-Java database query
Merge branch 'master' of https://github.com/bbuesser/RMG-Py
Add label saturateH to fromAdjacencyList()

- enables reading old Java-Style libraries for kinetics search on
website
Merge branch 'master' of https://github.com/bbuesser/RMG-Py