HumanBean17 · HumanBean17 · May 14, 2026 · May 13, 2026
@@ -94,7 +94,7 @@ java-codebase-rag init --source-root /path/to/java/repo --index-dir /path/to/.ja
 
 ### `increment`
 
-Runs cocoindex **catch-up** without a full Lance reprocess. **Does not** rebuild Kuzu. Every run prints a **multi-line stderr warning** that graph navigation may be stale until you run `reprocess` (see [`propose/CLI-SCENARIOS-PROPOSE.md`](../propose/CLI-SCENARIOS-PROPOSE.md) Appendix A for the contract).
+Runs cocoindex **catch-up** without a full Lance reprocess. **Does not** rebuild Kuzu. Every run prints a **multi-line stderr warning** that graph navigation may be stale until you run `reprocess` (see [`propose/completed/CLI-SCENARIOS-PROPOSE.md`](../propose/completed/CLI-SCENARIOS-PROPOSE.md) Appendix A for the contract).
 
 ```bash
 java-codebase-rag increment --source-root /path/to/java/repo --index-dir /path/to/.java-codebase-rag --quiet

@@ -1,12 +1,12 @@
 # Cursor task prompts — CLI scenarios (PR-CLI-1 → PR-CLI-3)
 
 Status: **active**. Implements
-[`plans/PLAN-CLI-SCENARIOS.md`](./PLAN-CLI-SCENARIOS.md) and
-[`propose/CLI-SCENARIOS-PROPOSE.md`](../propose/CLI-SCENARIOS-PROPOSE.md).
+[`plans/completed/PLAN-CLI-SCENARIOS.md`](./PLAN-CLI-SCENARIOS.md) and
+[`propose/completed/CLI-SCENARIOS-PROPOSE.md`](../propose/completed/CLI-SCENARIOS-PROPOSE.md).
 
 One prompt per PR. Each is **self-contained**: copy the prompt verbatim into
 Cursor, attach the files listed in its `@-files` block, and execute in agent
-mode. If this prompt disagrees with **`plans/PLAN-CLI-SCENARIOS.md`**, the plan
+mode. If this prompt disagrees with **`plans/completed/PLAN-CLI-SCENARIOS.md`**, the plan
 wins.
 
 **Workflow per PR**
@@ -34,22 +34,22 @@ wins.
 
 **Branch:** `chore/cli-scenarios-propose-approval` off `master`.  
 **Base:** `master`.  
-**Plan section:** `plans/PLAN-CLI-SCENARIOS.md` § PR-CLI-1.  
+**Plan section:** `plans/completed/PLAN-CLI-SCENARIOS.md` § PR-CLI-1.  
 **Estimated diff size:** 1 file, ~10 LOC.
 
 **Attach (`@-files`):**
 
-- `@plans/PLAN-CLI-SCENARIOS.md` (PR-CLI-1 section only)
-- `@propose/CLI-SCENARIOS-PROPOSE.md`
+- `@plans/completed/PLAN-CLI-SCENARIOS.md` (PR-CLI-1 section only)
+- `@propose/completed/CLI-SCENARIOS-PROPOSE.md`
 
 **Prompt:**
 
 ````
-You are implementing PR-CLI-1 from `plans/PLAN-CLI-SCENARIOS.md`.
+You are implementing PR-CLI-1 from `plans/completed/PLAN-CLI-SCENARIOS.md`.
 
 ## Scope
 
-- Update `propose/CLI-SCENARIOS-PROPOSE.md` **status** from **draft** to **approved**
+- Update `propose/completed/CLI-SCENARIOS-PROPOSE.md` **status** from **draft** to **approved**
   (or the repo’s equivalent convention) if reviewers have signed off.
 - Ensure **Appendix A** still states that the real issue URL is filled in **PR-CLI-2**
   (placeholder or canonical remote note — do not invent a final URL here).
@@ -71,7 +71,7 @@ None (documentation only).
 
 ## Sentinel checks
 
-- `git diff master --name-only` should list **only** `propose/CLI-SCENARIOS-PROPOSE.md`
+- `git diff master --name-only` should list **only** `propose/completed/CLI-SCENARIOS-PROPOSE.md`
   (or be empty if already merged).
 
 ## Manual evidence
@@ -92,16 +92,16 @@ N/A.
 **Branch:** `feat/cli-scenarios` off `master` (after PR-CLI-1 is on `master`, or
 stack if your team allows).  
 **Base:** `master` (contains merged PR-CLI-1).  
-**Plan section:** `plans/PLAN-CLI-SCENARIOS.md` § PR-CLI-2 + **Resolved design
+**Plan section:** `plans/completed/PLAN-CLI-SCENARIOS.md` § PR-CLI-2 + **Resolved design
 decisions** table.  
-**Propose:** `propose/CLI-SCENARIOS-PROPOSE.md` §3, §7, Appendix A (warning text).  
+**Propose:** `propose/completed/CLI-SCENARIOS-PROPOSE.md` §3, §7, Appendix A (warning text).  
 **Estimated diff size:** ~25–40 files, large LOC (single atomic PR; prefer
 sequential commits per concern inside the branch).
 
 **Attach (`@-files`):**
 
-- `@plans/PLAN-CLI-SCENARIOS.md`
-- `@propose/CLI-SCENARIOS-PROPOSE.md`
+- `@plans/completed/PLAN-CLI-SCENARIOS.md`
+- `@propose/completed/CLI-SCENARIOS-PROPOSE.md`
 - `@user_rag/cli.py` (pre-rename; becomes `java_codebase_rag/cli.py`)
 - `@server.py`
 - `@java_index_flow_lancedb.py`
@@ -122,10 +122,10 @@ sequential commits per concern inside the branch).
 **Prompt:**
 
 ````
-You are implementing PR-CLI-2 from `plans/PLAN-CLI-SCENARIOS.md`.
+You are implementing PR-CLI-2 from `plans/completed/PLAN-CLI-SCENARIOS.md`.
 
 Read the **PR-CLI-2** section and the **Resolved design decisions** table in full.
-Cross-check behaviour with `propose/CLI-SCENARIOS-PROPOSE.md` §3 / §7 / Appendix A.
+Cross-check behaviour with `propose/completed/CLI-SCENARIOS-PROPOSE.md` §3 / §7 / Appendix A.
 If this prompt and the plan disagree, the plan wins.
 
 ## Scope
@@ -274,14 +274,14 @@ production code paths must use the consolidated model.
 
 **Branch:** `chore/cli-scenarios-docs` off `master` (after PR-CLI-2 merged).  
 **Base:** `master`.  
-**Plan section:** `plans/PLAN-CLI-SCENARIOS.md` § PR-CLI-3; propose §6 (doc list +
+**Plan section:** `plans/completed/PLAN-CLI-SCENARIOS.md` § PR-CLI-3; propose §6 (doc list +
 acceptance grep + agent rules audit).  
 **Estimated diff size:** ~15–25 files, mostly markdown.
 
 **Attach (`@-files`):**
 
-- `@plans/PLAN-CLI-SCENARIOS.md` (PR-CLI-3 section)
-- `@propose/CLI-SCENARIOS-PROPOSE.md` (§6)
+- `@plans/completed/PLAN-CLI-SCENARIOS.md` (PR-CLI-3 section)
+- `@propose/completed/CLI-SCENARIOS-PROPOSE.md` (§6)
 - `@README.md`
 - `@AGENTS.md`
 - `@CODEBASE_REQUIREMENTS.md`
@@ -295,8 +295,8 @@ acceptance grep + agent rules audit).
 **Prompt:**
 
 ````
-You are implementing PR-CLI-3 from `plans/PLAN-CLI-SCENARIOS.md` and
-`propose/CLI-SCENARIOS-PROPOSE.md` §6.
+You are implementing PR-CLI-3 from `plans/completed/PLAN-CLI-SCENARIOS.md` and
+`propose/completed/CLI-SCENARIOS-PROPOSE.md` §6.
 
 ## Scope
 

@@ -1,8 +1,8 @@
 # Plan: CLI scenarios — lifecycle verbs, config consolidation, naming
 
-Status: **active**. This plan implements
-[`propose/CLI-SCENARIOS-PROPOSE.md`](../propose/CLI-SCENARIOS-PROPOSE.md).
-**PR-CLI-1** (propose approval + plan tracking) is [#72](https://github.com/HumanBean17/java-codebase-rag/pull/72); merge that PR to `master` to close the gate on mainline.
+Status: **completed — shipped** to `master`. This plan implemented
+[`propose/completed/CLI-SCENARIOS-PROPOSE.md`](../propose/completed/CLI-SCENARIOS-PROPOSE.md).
+**PR-CLI-1** (propose approval + plan tracking) was [#72](https://github.com/HumanBean17/java-codebase-rag/pull/72).
 
 Depends on: **none** (engine work for Kuzu incremental rebuild stays under
 [`propose/TIER2-INCREMENTAL-REBUILD-PROPOSE.md`](../propose/TIER2-INCREMENTAL-REBUILD-PROPOSE.md)
@@ -37,7 +37,7 @@ before PR-CLI-2 so contributors exercising new subcommands do not pay multi-seco
   **`CODEBASE_REQUIREMENTS.md`**, **`.cursor/rules/*.mdc`**, selected **`propose/*.md`**,
   **`mcp.json.example`** (comment polish only; keys land in PR-CLI-2), **`paper.pdf`**
   rebuild, plus **acceptance grep** / agent-rules audit per
-  [`propose/CLI-SCENARIOS-PROPOSE.md`](../propose/CLI-SCENARIOS-PROPOSE.md) §6. **PR-CLI-2**
+  [`propose/completed/CLI-SCENARIOS-PROPOSE.md`](../propose/completed/CLI-SCENARIOS-PROPOSE.md) §6. **PR-CLI-2**
   does **not** replace this: it ships code + `mcp.json.example` keys; a full doc
   sweep is explicitly **out of scope** for PR-CLI-2 (see PR-CLI-2 Definition of done).
 - **No ontology bump** and **no Kuzu / Lance schema changes** — this is operator
@@ -71,7 +71,7 @@ before PR-CLI-2 so contributors exercising new subcommands do not pay multi-seco
 
 | PR | Scope | Ontology bump | Files touched (approx) | Test buckets | Independent of |
 | --- | --- | --- | --- | --- | --- |
-| **PR-CLI-1** | Land / freeze propose (doc-only merge of `CLI-SCENARIOS-PROPOSE.md` if not already on `master`) | none | `propose/CLI-SCENARIOS-PROPOSE.md` (status bump); `plans/PLAN-CLI-SCENARIOS.md` (tracking) | n/a | none |
+| **PR-CLI-1** | Land / freeze propose (doc-only merge of `CLI-SCENARIOS-PROPOSE.md` if not already on `master`) | none | `propose/completed/CLI-SCENARIOS-PROPOSE.md` (status bump); `plans/completed/PLAN-CLI-SCENARIOS.md` (tracking) | n/a | none |
 | **PR-CLI-2** | Full implementation: lifecycle handlers, env + YAML + index layout, package rename, `server.py` / indexer / path helpers, **`mcp_v2.py`**, **`path_filtering.py`** (`.lancedb-mcp/ignore` → `.java-codebase-rag/ignore`), help redesign, tracking issue constant, user-visible stderr hints; **`mcp.json.example`** env keys = source of truth | none | `pyproject.toml`, package dir rename, `server.py`, `mcp_v2.py`, `java_codebase_rag/cli.py`, `java_index_flow_lancedb.py`, `graph_enrich.py`, `path_filtering.py`, `search_lancedb.py`, `kuzu_queries.py`, `build_ast_graph.py`, tests, `mcp.json.example`, `.gitignore`, any other `user_rag` / env / path references in Python | unit + integration + help-structure test (see below) | PR-CLI-1 merged |
 | **PR-CLI-3** | Doc and example sweep + **`.cursor/rules/`** + migration sections + acceptance grep; **`mcp.json.example`** comment/example polish only (keys already correct from PR-CLI-2) | none | `README.md`, `docs/*`, `AGENTS.md`, `.cursor/rules/*.mdc`, `CODEBASE_REQUIREMENTS.md`, `mcp.json.example` (prose only if needed), selected `propose/*.md`, `.gitignore` notes | manual grep audit; `ruff` / `pytest` unchanged by docs | PR-CLI-2 merged |
 
@@ -101,7 +101,7 @@ Landing order: **PR-CLI-1 → PR-CLI-2 → PR-CLI-3**.
 
 ## File-by-file changes
 
-### 1. `propose/CLI-SCENARIOS-PROPOSE.md`
+### 1. `propose/completed/CLI-SCENARIOS-PROPOSE.md`
 
 - Set status from **draft** to **approved** (or equivalent) once reviewers sign off.
 - Ensure Appendix A issue URL placeholder is clearly marked as filled in PR-CLI-2
@@ -121,7 +121,7 @@ Landing order: **PR-CLI-1 → PR-CLI-2 → PR-CLI-3**.
 
 | # | Step | File(s) | Done when |
 | --- | --- | --- | --- |
-| 1 | Review & merge propose | `propose/CLI-SCENARIOS-PROPOSE.md`; plan tracking in this file | [#72](https://github.com/HumanBean17/java-codebase-rag/pull/72) merged to `master` |
+| 1 | Review & merge propose | `propose/completed/CLI-SCENARIOS-PROPOSE.md`; plan tracking in this file | [#72](https://github.com/HumanBean17/java-codebase-rag/pull/72) merged to `master` |
 
 ---
 
@@ -359,5 +359,5 @@ Add **Migration from legacy names** sections with explicit `mv` commands
 
 - `PR-CLI-1`: **done (awaiting `master` merge)** — [#72](https://github.com/HumanBean17/java-codebase-rag/pull/72) (propose **approved** + this plan’s tracking update)
 - `PR-CLI-2`: **implemented (awaiting merge to `master`)** — lifecycle CLI + config consolidation in tree
-- `PR-CLI-3`: **in review** — `chore/cli-scenarios-docs`: README / docs / `AGENTS.md` / `.cursor/rules/` / migration / `paper.pdf` rebuild; mark **merged** when the PR lands on `master` (acceptance grep per `propose/CLI-SCENARIOS-PROPOSE.md` §6)
+- `PR-CLI-3`: **in review** — `chore/cli-scenarios-docs`: README / docs / `AGENTS.md` / `.cursor/rules/` / migration / `paper.pdf` rebuild; mark **merged** when the PR lands on `master` (acceptance grep per `propose/completed/CLI-SCENARIOS-PROPOSE.md` §6)
 - `Kuzu incremental tracking issue`: **opened** — [#73](https://github.com/HumanBean17/java-codebase-rag/issues/73) (Tier 2 engine scope; URL matches `KUZU_INCREMENTAL_TRACKING_ISSUE_URL` in `java_codebase_rag/cli.py`)
@@ -1,7 +1,7 @@
 # Plan: reprocess selective phase rebuild (`--vectors-only` / `--graph-only`)
 
-Status: **active (planning)**. This plan implements
-[`propose/REPROCESS-SPLIT-PROPOSE.md`](../propose/REPROCESS-SPLIT-PROPOSE.md).
+Status: **completed — shipped** to `master`. This plan implemented
+[`propose/completed/REPROCESS-SPLIT-PROPOSE.md`](../propose/completed/REPROCESS-SPLIT-PROPOSE.md).
 
 Depends on: **none**.
 
@@ -136,19 +136,19 @@ Landing order: **RS1**.
 
 ## Definition of done (PR-RS1)
 
-- [ ] `reprocess --help` shows mutually-exclusive selective flags.
-- [ ] `--vectors-only` runs only cocoindex full reprocess path and never invokes graph builder.
-- [ ] `--graph-only` runs only graph builder and never invokes cocoindex.
-- [ ] Selective success emits one drift warning to stderr naming the non-rebuilt store.
-- [ ] JSON payload includes `phases_run` with values matching phases actually spawned.
-- [ ] Graph-only build failure exits with code `1` (not `2`).
-- [ ] Selective setup failures exit with code `2`, emit no drift warning, and report
+- [x] `reprocess --help` shows mutually-exclusive selective flags.
+- [x] `--vectors-only` runs only cocoindex full reprocess path and never invokes graph builder.
+- [x] `--graph-only` runs only graph builder and never invokes cocoindex.
+- [x] Selective success emits one drift warning to stderr naming the non-rebuilt store.
+- [x] JSON payload includes `phases_run` with values matching phases actually spawned.
+- [x] Graph-only build failure exits with code `1` (not `2`).
+- [x] Selective setup failures exit with code `2`, emit no drift warning, and report
       `phases_run=[]`.
-- [ ] No-flag cocoindex failure reports `phases_run=["vectors"]` because graph was
+- [x] No-flag cocoindex failure reports `phases_run=["vectors"]` because graph was
       not spawned.
-- [ ] TTY pretty output for selective success includes `Rebuilt:` and `Skipped:`.
-- [ ] No-flag `reprocess` lifecycle test remains green.
-- [ ] `.venv/bin/python -m pytest tests/test_java_codebase_rag_cli.py -q` passes.
+- [x] TTY pretty output for selective success includes `Rebuilt:` and `Skipped:`.
+- [x] No-flag `reprocess` lifecycle test remains green.
+- [x] `.venv/bin/python -m pytest tests/test_java_codebase_rag_cli.py -q` passes.
 
 ## Implementation step list
 
@@ -160,6 +160,8 @@ Landing order: **RS1**.
 | 4 | Add/adjust CLI docs | `docs/JAVA-CODEBASE-RAG-CLI.md`, `README.md` | Docs match new CLI behavior, warning policy, argparse error shape, and default-vs-selective wording |
 | 5 | Add selective CLI tests | `tests/test_java_codebase_rag_cli.py` | New tests pass locally and anchor exit-code semantics |
 
+All rows landed on `master` (PR-RS1).
+
 ---
 
 # Cross-PR risks and mitigations
@@ -197,4 +199,4 @@ Landing order: **RS1**.
 
 # Tracking
 
-- `PR-RS1`: _pending_
+- `PR-RS1`: **landed** on `master` (selective `reprocess`, `phases_run`, docs, CLI tests).
@@ -1,6 +1,6 @@
 # Proposal: Smart `refresh_code_index` Mode Selection
 
-> **Note (2026):** the operator CLI’s full rebuild verb is now `java-codebase-rag reprocess` (see `propose/CLI-SCENARIOS-PROPOSE.md`); this MCP-side proposal still refers to `refresh_code_index` by name.
+> **Note (2026):** the operator CLI’s full rebuild verb is now `java-codebase-rag reprocess` (see `propose/completed/CLI-SCENARIOS-PROPOSE.md`); this MCP-side proposal still refers to `refresh_code_index` by name.
 >
 > For embeddings or search over raw `propose/` text, expect both that historical MCP name and current CLI wording in the same document until this draft is implemented or archived under `propose/completed/`.
 

@@ -1,6 +1,6 @@
 # CLI-SCENARIOS — restructure `java-codebase-rag` CLI, config, and naming
 
-**Status**: approved — signed off for implementation via §6 (PR-CLI-2 / PR-CLI-3).
+**Status**: completed — shipped (lifecycle verbs, config consolidation, package rename; plan closed under `plans/completed/PLAN-CLI-SCENARIOS.md`).
 **Author**: Dmitriy Teriaev + Perplexity Computer
 **Date**: 2026-05-10
 

@@ -1,6 +1,6 @@
 # REPROCESS-SPLIT — Make `reprocess` selectively rebuild vectors and/or graph
 
-**Status**: under review
+**Status**: completed — shipped (`reprocess --vectors-only` / `--graph-only`, `phases_run`, drift warnings, docs, and CLI tests on `master`).
 **Author**: Dmitriy Teriaev + Perplexity Computer
 **Date**: 2026-05-12 (revised 2026-05-13 after review)