With the previous TMWorkspace API it was possible to make the workspace
inconsistent by e.g. removing source files and forgetting to update
workspace. This could lead to non-obvious and not immediately visible
crashes.

The new set of the public (but also Geany private) API calls always
updates the workspace accordingly and neither of the calls can lead
to an inconsistent state of the workspace.

In addition, perform some minor cleanups and simplifications - unify
parsing from buffer and from file, support "parsing" of 0-sized buffers
and improve documentation.