Make database accessible

[mrp089]

Currently, simulation meta-information (boundary conditions, time-stepping, category, ...) are only accessible through reading locally saved .tcl files. This means that large parts of the code don't work without that local database.

To eliminate the need for a local database, do the following:

• create a script to extract all .tcl information, put it in one file, and add to the repository
• change existing scripts to only use the database file
• since large files (geometry, simulation results, ...) can't be added to the repository, find a way to synchronize these between the local disk and a remote server (skalak, sherlock, ...)
• change all scripts to not use any local information