Fix verified graph identity and clustering bugs

[forhappy]

Problem

Six open reports from jeanmonet reproduced valid bugs in incremental community clustering, hierarchy IDs, HTML/Markdown/R identities and links, and empty Bash files.

Changes

• Recluster prior communities that have become disconnected, including when their source files are unchanged.
• Keep reconciled hierarchy IDs unique with deterministic bounded disambiguation; continue reading known hierarchy-signature/v1 artifacts.
• Preserve full Markdown row identity, exact R function names and nested lexical scopes, and publish empty Bash files without a zero-range entrypoint.
• Give HTML table occurrences distinct IDs, originate references at their <a>/<link> occurrence, and count but omit self-links.
• Add regression tests and document cache/publication identity changes.

Compatibility

The AST cache version advances to 16 and graph publication semantics to /2. The graph schema remains /1; Markdown table row/cell and HTML table/row IDs change on rebuild. Hierarchy signature v2 is emitted while known v1 artifacts remain readable. Historical realizations are not rewritten.

Verification

• cargo fmt --all -- --check and git diff --check passed.
• cargo clippy --workspace --lib --bins --locked -- -D warnings passed.
• cargo test --workspace --lib --bins --locked passed; two tests were ignored.
• Targeted community, hierarchy, Markdown, HTML, R, and Bash regressions passed.
• scripts/qualify_code_graph_v1.sh --fixtures-only validated the strict manifests and passed five of six scale checks. Its framework-resolution ceiling test took 189 seconds against a 90-second limit while other Cargo builds were active. The script stopped before the React fixture step.

Fixes #346
Fixes #347
Fixes #348
Fixes #349
Fixes #350
Fixes #351