Revise exclude patterns behaviour and docs

[lukpueh]

Description of issue or feature request:
in-toto-run CLI and API take an "exclude pattern" argument to match file paths, which should be excluded from resulting link metadata.

While setting up an in-toto pipeline (tuf#2000) and also while refactoring related code (#584) I noticed a few issues, which are randomly listed below.

Current behavior:

• Our docs on RTD alone do not suffice to understand proper usage, and might be inaccurate too (former is my personal experience from setting up the tuf pipeline mentioned above; latter needs checking!)
• There are some opinionated default patterns settings.ARTIFACT_EXCLUDE_PATTERNS, which are used rather in-transparently.
• What's the expected pattern to exclude dotfiles in CWD, i.e. when ["."] is passed as materials or products argument?
• Should we, in terms of expected/intuitive behavior, pattern-match before or after:
  • changing base path (currently after)
  • stripping ITE-4 schemes (currently after)
  • applying os.path.normpath (currently after; does this make patterns platform-dependent?)
  • constructing the file path, i.e. dirpath + basename (currently before and after)
  • removing lstrip paths (currently before)
  • replacing backwards with forward slashes (currently before; also see #565)
• It could be helpful to allow different patterns for materials and products.

Expected behavior:

1. Agree on expected/intuitive behavior
2. Make sure the implementation is correct
3. Update docs to be useful

NOTE: I strongly suggest to fix issues based on the refactor in #584, which drastically simplifies the code, w/o changing prior behavior.