Move include/exclude files lists to projects (CODE_DIR/.autopilot)

[hatkyinc2]

Move include/exclude files lists to projects (CODE_DIR/.autopilot)

Probably some project/.autopilot/config
Assuming we want one autopilot to run on many projects and we want to use a -d to look at different projects, they need to have their own config.
That config should be shared between users of autopilot if there are any.
This is a common pattern for coding tools. (code validators, CI etc)

while currently this ticket talks about the existing include/exclude lists, we see the future use of this directory in other tasks
the local DB file and/or vector DB.(#70, #69)
testing/validation parameters. (#75)

[hatkyinc2]

See #164 instead