…ks.json (#143 #389) (#390)

* feat: add entry-reference extractor (shared discovery for #143 + #68/#69)

Pure parser over a Benchling entry dict that surfaces the objects an entry
points at, in one place for both upcoming features:

- extract_entity_references(): entity IDs from days[].notes[].links[]
  (filtered to entity types, dropping non-entity links like sql_dashboard)
  and from entity-link fields; deduped by ID. -> #143 entity packaging.
- extract_results_tables(): results_table notes carrying assayResultSchemaId.
  -> #68/#69 assay results.
- extract_note_links(): low-level all-links primitive.

No Benchling API calls and no behavior change -- nothing consumes it yet, so
it lands independently of either feature. 13 unit tests; black/isort/pyright
clean.

Refs #143 #68

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat: full EntryLink type map + classify_links; fix entity set (#389)

Generalize the discovery layer from entities-only to the full EntryLink enum
(18 types from test/openapi.yaml), per #389.

- classify_links(entry): surfaces ALL note links, each labeled with a
  LinkCategory (entity/inventory/reference/metadata/not_packageable/uncertain/
  external/unknown). Consumers filter, e.g. `r.is_packageable`. Unknown/future
  types surface as UNKNOWN rather than being silently dropped.
- LINK_TYPE_CATEGORY: type -> category for all 18 tokens; PACKAGEABLE_CATEGORIES.
- Fix entity set: ENTITY_LINK_TYPES now {custom_entity, dna_sequence,
  aa_sequence, batch}. Adds `batch` (a real registry entity, was missed);
  drops dna_oligo/rna_oligo (NOT EntryLink types -- can't appear as note links).
- spec/entry-link-types.json: human-facing reference map (category, packageable,
  id prefix, GET endpoint, webhook events) for all 18 types, plus the
  not-inline-linkable resources. A test asserts its categories match the module
  so it can't drift.

26 unit tests; black/isort/pyright clean.

Refs #143 #389 #68

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat: write references.json into each package; address review

When packaging an entry, write a references.json alongside entry.json listing
the Benchling objects the entry points at (entities, classified links, results
tables), discovered from the entry's note links and fields. No records are
fetched -- discovery only.

- entry_references.summarize_references(entry): JSON-serializable payload
  ({schema_version, entities, links, results_tables}); REFERENCES_SCHEMA_VERSION.
- entry_packager._create_metadata_files: emit references.json + document it in
  the package README.

Review fixes (Greptile + Copilot):
- Drop empty-string entity IDs in _field_value_ids, matching the note-link guard.
- Narrow RESULTS_TABLE_NOTE_TYPES to {"results_table"} -- the only type carrying
  assayResultSchemaId; avoids latently capturing generic/registration tables.
- Modernize typing (dict/list/tuple) on the 3.11+ codebase.
- Remove committed spec/entry-link-types.json (relocated to the project's
  scripts/ as a research artifact) and its drift-guard test.

Full suite green (437).

Refs #143 #389 #68

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* test: regression test for empty-string entity-link field values

Confirms _field_value_ids drops empty strings (single + isMulti list),
matching the note-link guard. Requested in review.

Refs #143

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* refactor: replace overloaded `packageable` with fetchable + eventable + disposition

`packageable` conflated two questions: can a record be fetched, vs. should it
live in its own package or nested in the entry. Split into orthogonal axes and a
derived disposition.

- FETCHABLE_CATEGORIES (GET-by-id exists) + EVENTABLE_CATEGORIES (own webhooks,
  can arrive independent of an entry) + CATEGORY_DISPOSITION.
- LinkRef.is_fetchable / is_eventable / disposition (replaces is_packageable).
- references.json links now carry {category, fetchable, eventable, disposition}.

disposition makes explicit that nest-vs-standalone is a genuine product decision
ONLY for entities (fetchable AND eventable -> nest_or_standalone). Non-entities
are forced: inventory -> nest (no events); entry/request/workflow -> link (own
package); metadata -> pointer; dashboards/external -> skip.

Project artifact scripts/entry-link-types.json updated to match (not in repo).

Refs #143 #389

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat: searchable links metadata + raw links.json (entity name enrichment)

Promote a curated `links` array into entry.json (the package's metadata_uri)
so packages are searchable by the human-readable name of the entities/objects
an entry references — the top-line use case from the 2026-06-15 call ("show me
all experiments where QB-2743.1 was used").

Each curated link carries four fields, each with one job:
  - type, id  — free; id supports downstream linking
  - name      — authoritative Benchling display name via best-effort GET-by-id,
                or null when the lookup fails/isn't supported (never a slug)
  - slug      — lossy token parsed from the webURL, for eyeballing/debugging only

Verified the human name is NOT recoverable from the webURL: the trailing
segment is a lowercased, punctuation-flattened slug (sBN000 -> sbn000), so the
exact name must come from the API. Name resolution is best-effort and never
raises — it requires the app to be a registry/project collaborator.

Also rename references.json -> links.json and reduce it to raw facts only
(id/type/web_url + entities + results_tables). Derived classifications
(category/fetchable/eventable/disposition) are no longer persisted; they are
recomputed from type in code, so the raw archive stays reprocessable and a
future classification change needs no re-fetch. Schema bumped to v2.

Refs #143 #389

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* chore: bump version to 0.17.3

* docs: changelog for 0.17.3 (searchable links metadata + links.json)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* chore: bump version to 0.18.0

* docs: align changelog heading to 0.18.0

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: clarify note-link shape — id and webURL are optional

Note links carry a required type plus optional id (external link has none)
and optional webURL (e.g. location has none). Addresses PR #390 review.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>