Add `comment_type: markdown` for agent and skill definition files

[HartmannNico]

Motivation

AI agent and skill definition files (.claude/agents/*.md, .github/prompts/*.md, Copilot instruction files) are increasingly the primary implementation artefacts of agentic systems. They sit at the same layer as Rust or Python source files in a requirements → architecture → design → implementation traceability chain — but sphinx-codelinks currently has no comment_type that covers Markdown.

Without Markdown support, any design node whose implementation is a Markdown agent file cannot close its downstream implementation coverage in the graph. This blocks the traceability spine at precisely the point where AI-native projects need it most.

Proposed solution

Add comment_type: markdown backed by tree-sitter-markdown, using block-level HTML comments as the marker carrier:

<!-- @needs My agent realization, prd_unit_imp__thalam__agent_realization, prd_unit_imp, [prd_unit_des__thalam__agent_realization] -->

HTML comments are:

• Invisible in all Markdown renderers (GitHub, VS Code, Sphinx/MyST)
• Valid CommonMark — no extension required
• Git-diffable and grep-able in plain text

Implementation shape (3 files, ~24 lines)

tree-sitter-markdown maps standalone <!-- … --> blocks to html_block nodes. The tree-sitter query is simply (html_block) @comment.

source_discover/config.py

"markdown": ["md", "markdown"],     # COMMENT_FILETYPE
markdown = "markdown"               # CommentType enum

analyse/utils.py

MARKDOWN_QUERY = """(html_block) @comment"""

elif comment_type == CommentType.markdown:
    import tree_sitter_markdown
    parsed_language = Language(tree_sitter_markdown.language())
    query = Query(parsed_language, MARKDOWN_QUERY)

No SCOPE_NODE_TYPES entry needed — Markdown has no function/class scopes; oneline-only mode (get_oneline_needs=True, get_need_id_refs=False) never invokes scope association.

pyproject.toml

"tree-sitter-markdown>=0.5.1",

One caller-side note

Because html_block node text includes the full <!-- … --> delimiters, callers must set end_sequence: " -->" (not the default "\n") in their oneline_comment_style config. This is the only difference from all other comment_type entries and should be documented in the README example.

Precedent

Analogous to the bash comment_type (PR #92). PR #82 (TypeScript) is the structural template for this PR shape.