docs: keep file examples inside workspace

[EvanProgramming]

Fixes #54

Update shipped file examples and tool docstrings to use relative paths inside the active workspace. Add a README boundary note and a regression test that parses and executes the documented write_file/read_file JSON examples in a real temporary workspace.

Validation:

• ./venv/bin/python -m unittest tests.test_tools -v (10 tests, documented examples executed)
• make check
• make lint
• make test (130 tests)
• make docs-check
• make shell-check
• git diff --check
• PR head 602d159 is GPG-signed and GitHub verified.