Revise git and config copying in main.py

[Raymond Smith]

Without git, it searches for *.py files, but with the new structure and design to be run from outside of the repo, it can just do a full copy of the entire repo tree into the output directory if git is missing.

In addition, there are unhandled exceptions and out of date search paths for daetools.cfg files.

This should all be tested (maybe not in the test suite...) at least by running it in a clone in which the .git subdirectory has been removed.

[Raymond Smith]

The current behavior is okay for the *.py file copying, actually. It just brings all the *.py files within /mpet/*.py (the location of main.py), which is all that really needs to be copied.

Full copy of the repo tree is not okay given the move back to encouraging users to work within the root directory.

The exceptions and daetools.cfg search paths still need to be updated.

[Raymond Smith]

Fixed in commit 1e74c2c.