Add document workflows, entry graph links, and discovery/docs updates

docs/entry_graph.md

@@ -0,0 +1,53 @@
+# Entry Graph Links
+
+SeedPass now supports explicit relationships between entries, so your vault can evolve from tag clusters into a typed knowledge graph.
+
+## Link Model
+
+Every entry can include:
+
+- `links`: list of objects with:
+  - `target_id`: target entry index
+  - `relation`: link type (for example `references`, `depends_on`, `owned_by`, `derived_from`)
+  - `note`: optional free-form context
+
+Example:
+
+```json
+{
+  "links": [
+    { "target_id": 42, "relation": "references", "note": "Used by deploy script" }
+  ]
+}
+```
+
+## CLI Commands
+
+- Add link:
+  - `seedpass entry link-add --entry-id 1 --target-id 42 --relation references --note "Used by deploy script"`
+- List links:
+  - `seedpass entry links --entry-id 1`
+- Remove link:
+  - `seedpass entry link-remove --entry-id 1 --target-id 42 --relation references`
+- Replace full link list:
+  - `seedpass entry modify 1 --links-json '[{"target_id":42,"relation":"references","note":"Used by deploy script"}]'`
+
+## API Endpoints
+
+- `GET /api/v1/entry/{id}/links`
+- `POST /api/v1/entry/{id}/links`
+  - Body: `{ "target_id": 42, "relation": "references", "note": "..." }`
+- `DELETE /api/v1/entry/{id}/links`
+  - Body: `{ "target_id": 42, "relation": "references" }`
+- `PUT /api/v1/entry/{id}` also accepts a full `links` array for replacement.
+
+## Search and Sync Behavior
+
+- Search now matches link metadata (`relation`, `note`) and linked target labels.
+- Sync conflict resolution includes `links` in deterministic equal-timestamp union merge, alongside `tags` and `custom_fields`.
+
+## Recommended Conventions
+
+- Keep `relation` values short and consistent (`references`, `depends_on`, `owned_by`, `belongs_to`, `derived_from`).
+- Use `note` for human context instead of encoding meaning into long relation strings.
+- Use tags for broad grouping, links for explicit semantics.