utils: honour recursive glob patterns in _should_include (#275)

[filipchristiansen]

Previously, atomics/**/*.md and similar patterns never matched, because _should_include treated all patterns as fixed-depth globs.

This patch adds dedicated logic that distinguishes recursive (**) from non-recursive patterns and introduces directory-aware checks so we only descend into directories that could contain matches.

✅ Fixes: #275

⚠️ Known issue: the matcher now collects the correct .md files, but the directory-structure output still lists the directories themselves even when they contain no matched files (e.g. atomics/Indexes/Attack-Navigator-Layers/, atomics/T1003.003/src/). A follow-up PR will tackle this.

[Copilot]

Pull Request Overview

This PR updates the glob-matching logic in _should_include to properly handle recursive (**) patterns and avoid descending into directories that cannot match, while also updating development documentation and bumping hook versions.

• Distinguishes between recursive and non-recursive glob patterns and adjusts directory traversal accordingly
• Adds a ValueError for non-recursive patterns when directory depth is exceeded
• Updates CONTRIBUTING instructions with --reload and bumps pre-commit hook versions

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
src/gitingest/utils/ingestion_utils.py	Enhanced _should_include to support ** recursion and strict depth checks; added error raising and updated docstring
CONTRIBUTING.md	Added --reload flag to local server startup command
.pre-commit-config.yaml	Upgraded pyupgrade, markdownlint, and pylint hook versions

Comments suppressed due to low confidence (2)

src/gitingest/utils/ingestion_utils.py:113

• The TODO comment in _should_exclude indicates incomplete functionality. Either implement the intended behavior for ** in exclude patterns or open an issue to track this work and remove the placeholder.

TODO: Check if we need to handle exclude patterns with **, and if so, how.

src/gitingest/utils/ingestion_utils.py:69

• Consider adding unit tests to cover edge cases of both recursive (**) and non-recursive glob patterns, including directory-depth mismatches and patterns ending in /*, to ensure this new logic behaves as expected.

for pattern in include_patterns - {""}:  # ignore empty pattern