traverse_project: Better handle overlap between pyenv and code/deps dir

Issue #465 highlights a peculiar case where the top-level project
directory is also itself the root of a virtualenv. Our traversal code
will skip any (given or detected) Python environment, under the
assumption that we never want to analyze code/deps from a package
installed within. However, we here have a special case where -- from the
traversal code's POV -- we have found a pyenv rooted at a directory that
also appears in the given settings.code and/or settings.deps (by default
settings.code, settings.deps and settings.pyenvs are all ".").

Work around this special case as follows: When a Python environment is
found rooted at a path that is _also_ directly given in either
settings.code or settings.deps, then we _don't_ want to skip traversal
of the entire directory, rather we only skip traversal of the specific
subdirectories that form the actual contents of the environment:

 - Any package dirs found by validate_pyenv_source() (i.e. any
   "site-packages" dirs).
 - The "bin/" (or "Scripts\" on Windows) subdir where we expect to find
   any tools installed into the environment.

We could probably extend this handling to _any_ Python environment
(including those found after we start the traversal proper), but I'm not
100% sure that this won't trigger false positives where some weird
Python environment (e.g. a Conda or poetry2nix environment) happens to
contain extra "stuff" missing from the above list that would adversely
affect our analysis.

Author: jherland

fawltydeps/traverse_project.py

@@ -1,6 +1,7 @@
 """Traverse a project to identify appropriate inputs to FawltyDeps."""
 
 import logging
+import sys
 from collections.abc import Iterator
 from collections.abc import Set as AbstractSet
 from pathlib import Path
@@ -131,7 +132,18 @@ def find_sources(  # noqa: C901, PLR0912, PLR0915
         if package_dirs is not None:  # Python environment dir given directly
             logger.debug(f"find_sources() Found {package_dirs}")
             yield from package_dirs
-            traversal.skip_dir(path)  # disable traversal of path below
+            if path in (settings.code | settings.deps):
+                # We are also searching this dir for code/deps, hence we should
+                # not skip it altogether, but rather only skip the parts of it
+                # that likely contain installed 3rd-party packages
+                for pyenv_src in package_dirs:
+                    traversal.skip_dir(pyenv_src.path)
+                if sys.platform.startswith("win"):  # Windows
+                    traversal.skip_dir(path / "Scripts")
+                else:  # Assume POSIX
+                    traversal.skip_dir(path / "bin")
+            else:
+                traversal.skip_dir(path)  # disable traversal of entire Python env
         else:  # must traverse directory to find Python environments
             traversal.add(path, PyEnvSource)