Complete Phase 13 glossary module

docs/rewrite-notes.md

@@ -61,6 +61,10 @@ Implemented:
 - Production module-registry scaffolding with known key recognition and explicit unsupported/unimplemented errors.
 - Production grammar module package with Python-aligned prompt intent and guardrails.
 - Explicit `--modules grammar` runtime path through runner, shared proposal generation, validators, application, reporting, and diagnostics.
+- Production glossary module package with Python-aligned prompt intent and guardrails.
+- Glossary-derived deterministic protected-term extraction and validator integration.
+- Explicit `--modules glossary` runtime path through runner, shared proposal generation, validators, application, reporting, and diagnostics.
+- Repeated glossary stage support with deterministic instance names (`glossary_1`, `glossary_2`), including mutable working-transcript handoff.
 - Broad deterministic and CLI/subprocess test coverage for implemented phases through `go test ./...`.
 - Internal typed structured LLM contract (`StructuredLLMClient.CompleteStructured(ctx, req, out)`).
 - `internal/framework/llm` instructor-go-backed adapter with:
@@ -76,9 +80,9 @@ Implemented:
 - Generic JSON diagnostics primitives for LLM interactions (request metadata, request payload, response payload, optional error payload) with secret redaction.
 
 Not yet implemented in runtime pipeline:
-- Real correction modules for `glossary`, `homophones`, and `spoken_word`.
+- Real correction modules for `homophones` and `spoken_word`.
 - Domain proposal prompts for remaining real modules.
-- End-to-end transcript polishing behavior.
+- End-to-end transcript polishing behavior with the full default module sequence.
 
 ## Completed phases
 
@@ -216,7 +220,7 @@ Not implemented in Phase 8 (by design):
 
 ## Remaining work plan
 
-Next recommended phase: **Phase 13 (glossary module and protected-term behavior)**.
+Next recommended phase: **Phase 14 (homophones module)**.
 
 ## Phase 9: Structured LLM client and scheduler infrastructure
 
@@ -362,44 +366,28 @@ Not implemented in Phase 12 (by design):
 
 ## Phase 13: Glossary module and protected-term behavior
 
-### Purpose
+Completed.
 
-Implement the glossary correction module and the glossary-derived protection behavior needed by downstream modules.
+Implemented:
+- Production glossary module package in `internal/modules/glossary`.
+- Glossary prompt builder aligned to Python intent and constrained to glossary-supported domain/acoustic corrections.
+- Prompt context using glossary names, aliases, categories, summaries, and plural forms where available.
+- Glossary proposal generation through shared `internal/framework/proposal_generation` using `contracts.StructuredLLMClient`.
+- Scheduler-aware glossary proposal generation through existing scheduler hooks.
+- Glossary replacement policy `replace_all` (matching Python behavior).
+- Glossary validator chain using existing deterministic and LLM-backed validators.
+- Glossary confidence threshold enforcement through existing config + confidence-threshold validator behavior.
+- Deterministic glossary-derived protected-term extraction (`internal/framework/validators/protected_terms.go`) from names, aliases, and plural forms, with stable deduplicated ordering.
+- Protected-term validator behavior remaining available to non-glossary modules via existing deterministic validators.
+- Explicit runtime support for `--modules glossary` through normalization, chunking, runner, proposal generation, validation, application, and reporting.
+- Repeated glossary-stage support (`--modules glossary,glossary`) with deterministic instance naming and mutable working-transcript handoff across stages.
+- Prompt/response diagnostics artifacts for glossary proposal + validator interactions with secret redaction.
+- Module-level reports for glossary including generated proposals, validator decisions/rejections, applied changes, and application skips.
+- CLI/runtime fake-client tests for approved proposals, validator rejection, application skips, repeated stages, diagnostics, failure/error.log behavior, and report outputs (`--report-json` and run-dir `report.json`).
 
-### Scope
-
-Implement:
-- `glossary` module package.
-- Glossary prompt builder ported from Python.
-- Glossary structured response model.
-- Glossary replacement policy.
-- Glossary confidence threshold handling.
-- Glossary validator chain.
-- Protected-term extraction from parsed glossary.
-- Protected-term validator behavior used by other modules where applicable.
-- Prompt/response diagnostics.
-- CLI support for `--modules glossary`.
-- Fake LLM tests.
-- Tests for repeated glossary stages using `glossary,glossary`.
-
-Do not implement:
-- Homophones module.
-- Spoken-word module.
-- Default full pipeline parity claim.
-
-### Expected behavior at end of phase
-
-Running `audita process ... --modules glossary` should perform real glossary-supported corrections. Repeated glossary stages should work and be reported as separate module instances.
-
-### Definition of done
-
-- Glossary module runs in the production runner.
-- Glossary terms and aliases are used in prompts and validators.
-- Protected-term behavior is implemented and tested.
-- Repeated glossary module instances are reported correctly.
-- Applied/skipped glossary changes appear in reports.
-- Prompt/response diagnostics are written.
-- `go test ./...` passes without requiring external LLM credentials.
+Not implemented in Phase 13 (by design):
+- Production `homophones` and `spoken_word` modules.
+- Full default module sequence execution as a feature-complete claim.
 
 ## Phase 14: Homophones module