Check and safeguard all the user-specified directories

[RodenLuo]

"difffit\tool.py", line 1825, in sim_button_clicked
for file_name in sorted(os.listdir(str_dir)):
^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [WinError 3] The system cannot find the path specified:
'split_out'

v0.7.0

See https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16716 for more.