fix(core): remove regular-file permalink lookup

[phernandez]

Summary

Remove the discarded permalink lookup from regular-file indexing and make the existing non-Markdown identity contract explicit.

Non-Markdown resources continue to be addressed by their stable external_id and project-relative file_path. They continue to persist with permalink=None.

Fixes #1182.

Problem

BatchIndexer._upsert_regular_file() called EntityService.resolve_permalink() when creating a PDF, image, or other non-Markdown entity, then discarded the returned value and created the entity without a permalink.

That call was dead work, but it also obscured an important domain invariant: permalinks are semantic addresses for Markdown notes because they can round-trip through frontmatter. A generated database-only permalink for arbitrary resource bytes would introduce a second identity that the source cannot represent.

Implementation

• Remove the unused resolve_permalink() call from the regular-file creation path.
• Document that non-Markdown entities always have permalink=None.
• Document the intended identities:
  • external_id is the stable API identity.
  • file_path locates the resource in project storage.
• Strengthen the existing batch-indexer regression so PDF and image indexing:
  • fails immediately if permalink resolution is attempted;
  • asserts both entities persist with no permalink.

Scope

This is contract cleanup only. It does not:

• add or backfill non-Markdown permalinks;
• change routing, search, relation resolution, or wikilinks;
• change regular-file move/update/delete behavior;
• change Markdown permalink behavior.

Verification

• uv run pytest -q --no-cov tests/indexing/test_batch_indexer.py::test_batch_indexer_indexes_non_markdown_files tests/index/test_local_project_index.py::test_local_project_index_indexes_regular_files tests/index/test_local_project_index.py::test_local_project_index_updates_regular_file_checksum tests/index/test_local_project_index.py::test_local_project_index_moves_and_deletes_regular_file_entities tests/index/test_local_project_index.py::test_local_project_index_resolves_regular_file_relations tests/index/test_local_watch_regular_file_parity.py
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