Fixes bug where logs do not properly get updated in significant size simulations.

[CodeByDrescher]

Identified two sibling race conditions causing logs to be inaccurate under certain circumstances:

If VCell CLI ran a "heavier" simulation, it would encounter one of two different race conditions:

1. Java attempts to move the "final" log files from the temporary directory to the actual output directory, however python was not yet finished editing the file.
2. Java attempts to forcefully close the python shell it was using, before python had the chance to update the logs.

Both cases have been remedied.