feat: add a manual compendium for hand-curated cliques, EUPATH seed term, and source docs

[SkyeAv]

Adds a manual compendium for hand-curated identifiers, seeds it with EUPATH:0009259 ("Shannon-indexed alpha diversity data"), supports future multi-CURIE manual cliques via equivalents, and documents both the reusable manual mechanism and the current EUPATH example.

Manual Compendium

• Adds input_data/manual_terms.ndjson as the source of truth for hand-curated entries.
• Adds src/createcompendia/manual.py and src/snakefiles/manual.snakefile to materialize per-prefix labels/synonyms files and build Manual.txt.
• Supports optional equivalents so one NDJSON row can form a single multi-CURIE clique while keeping the primary curie first.
• Rejects overlapping manual cliques by raising on identifiers that appear in more than one row.
• Passes manual prefixes through extra_prefixes so novel prefixes survive NodeFactory.
• The manual compendium is part of the normal build: Snakefile and src/snakefiles/util.py always register Manual.txt in the compendium, synonym-export, report, KGX, DuckDB, and sapbert paths.

Documentation

• Adds docs/sources/MANUAL/README.md for the reusable manual-ingestion path.
• Adds docs/sources/EUPATH/README.md for the current EUPATH manual entry.
• Updates docs/sources/README.md so the new docs are discoverable alongside existing source docs like ENSEMBL and UMLS (the source-doc index is linked from AGENTS.md).

Testing

• Adds targeted unit coverage in tests/createcompendia/test_manual.py for:
  • NDJSON parsing
  • singleton and multi-CURIE clique construction
  • equivalent deduplication
  • duplicate-identifier rejection
  • labels/synonyms materialization
• Adds aggregator-registration coverage, consolidated into tests/test_snakefile_util.py alongside the existing duckdb_memory_limit_mb tests.
• Verification:
  • uv run pytest -m unit --no-cov -q -> 412 passed, 105 deselected
  • uv run rumdl check . -> passed
  • uv run snakemake -c 1 -n manual resolves the manual / manual_compendia / manual_labels_synonyms DAG with no extra config

[hyi]

@SkyeAv I took a quick look at this PR and it looks good to me, so I am approving it. However, please wait for approval from @gaurav before merging.

[SkyeAv]

@gaurav should I want until I can build BABEL before continuing with this? I think I should probably merge current main to this branch and rebase my changes before merging sometime.

[SkyeAv]

@gaurav regardless of if you merge the PR please let me know what you end up choosing to do with the unstable code so I can both update this PR and also change the development model moving forward

[SkyeAv]

@gaurav Dropped the unstable flag — the manual compendium is no longer opt-in. Manual.txt now builds as part of the normal pipeline (the unstable_enabled() helper, the config["unstable"] toggle, the --config unstable=true gating, and the related docs/tests are all removed). Title and description updated to match.