looking fo documentation for module files

[Skaperen]

Output:
lt1a/forums/3 /home/forums 7> python3.8 -S -c "import sys; print(sys.prefix, sys.exec_prefix, sys.base_exec_prefix)"
/usr /usr /usr
lt1a/forums/3 /home/forums 8>

This means that before the import of the 'site' module, the prefixes are CORRECT! They get corrupted somewhere when you run without the -S option. Try this perhaps

Output:
python3.8 -S -c "import site; print(site.PREFIXES)"

and compare with

Output:
python3.8 -S -c "import site; site.main(); print(site.PREFIXES)"

Output:
lt1a/forums/1 /home/forums 47> python3.8 -S -c "import site; print(site.PREFIXES)"
['/usr', '/usr']
lt1a/forums/1 /home/forums 48> python3.8 -S -c "import site; site.main(); print(site.PREFIXES)"
['/usr', '/usr']
lt1a/forums/1 /home/forums 49>

looks the same and correct to me.