instances2matrix.py: various fixes

* database and collection are now command line arguments instead of options
* added option to reset collections
matrix2pmi.py: various fixes

* added option to reset collections
* fixed bug in make_F_all() status messages
* fixed bug in --start=F_ip option handling
added utility for converting reverb data to matrix input instances
.gitignore: ignore mongodb data, logs and such
refactored test data adding seeds
committed initial test script