refactor(levelup): revert CDR storage to markdown

- /levelup.init outputs to {PROJECT}/.specify/memory/cdr.md
- /levelup.clarify reads/writes .specify/memory/cdr.md
- /levelup.skills validates only Accepted CDRs
- /levelup.implement extracts accepted CDRs to {TEAM_DIRECTIVES}/CDR.md
- Added CDR_FILE to setup-levelup scripts
- Bump version to 0.0.127

Author: kanfil

CHANGELOG.md

@@ -7,6 +7,18 @@ All notable changes to the Specify CLI and templates are documented here.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to to [Semantic Versioning](https://semver.org/spec/v2.0.0/).
 
+## [0.0.127] - 2026-03-13
+
+### Changed
+
+- **Breaking**: Reverted CDR storage from JSON to markdown
+  - `/levelup.init` now outputs to `{PROJECT}/.specify/memory/cdr.md` (local)
+  - `/levelup.clarify` reads/writes `.specify/memory/cdr.md`
+  - `/levelup.skills` validates only CDRs with status "Accepted"
+  - `/levelup.implement` copies only accepted CDRs to `{TEAM_DIRECTIVES}/CDR.md` (root)
+  - Added `CDR_FILE` to setup-levelup scripts output
+  - Removed status field from `.skills.json` references
+
 ## [0.0.126] - 2026-03-12
 
 ### Changed

extensions/levelup/commands/clarify.md

@@ -37,9 +37,9 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 Resolve ambiguities in discovered or proposed CDRs through **clarifying questions**. Update module statuses based on answers.
 
-**Input**: Modules from `{TEAM_DIRECTIVES}/.cdrs.json` with status "discovered" or "proposed"
+**Input**: CDRs from `{REPO_ROOT}/.specify/memory/cdr.md` with status "Discovered" or "Proposed"
 
-**Output**: Updated modules with refined content and new statuses in `.cdrs.json`
+**Output**: Updated CDRs with refined content and new statuses in `.specify/memory/cdr.md`
 
 **Key Concept**:
 
@@ -105,11 +105,11 @@ Or set: export SPECIFY_TEAM_DIRECTIVES=/path/to/team-ai-directives
 
 #### Step 1: Load CDRs
 
-Read `{TEAM_DIRECTIVES}/.cdrs.json` and parse all modules.
+Read `{REPO_ROOT}/.specify/memory/cdr.md` and parse all CDRs.
 
 Filter modules by status:
-- **Primary**: Status = "discovered" or "proposed"
-- **Skip**: Status = "accepted", "active", "deprecated"
+- **Primary**: Status = "Discovered" or "Proposed"
+- **Skip**: Status = "Accepted", "Rejected", "Deprecated"
 
 If user specified specific module IDs, filter to those.
 
@@ -247,33 +247,30 @@ If content needs revision:
 
 ### Phase 5: Update Modules
 
-**Objective**: Write updated modules to `.cdrs.json`
+**Objective**: Write updated CDRs to `.specify/memory/cdr.md`
 
-#### Step 1: Update Module File
+#### Step 1: Update CDR File
 
-Update `{TEAM_DIRECTIVES}/.cdrs.json` for each clarified module:
+Update `{REPO_ROOT}/.specify/memory/cdr.md` for each clarified CDR:
 
-1. Update status field
+1. Update status in the CDR index table
 2. Add or update content if revised
-3. Add clarification metadata:
+3. Add clarification metadata in the CDR section:
 
-```json
-{
-  "modules": {
-    "{module-id}": {
-      "path": "context_modules/rules/{domain}/{file}.md",
-      "type": "rule",
-      "status": "accepted",
-      "clarification": {
-        "date": "2026-03-12",
-        "validation": "{validity answer}",
-        "scope": "{scope answer}",
-        "priority": "{priority answer}",
-        "changes": ["{list of changes}"]
-      }
-    }
-  }
-}
+```markdown
+### CDR-{ID}: {Title}
+
+**Status**
+
+**Accepted** | Proposed | Rejected
+
+### Clarification
+
+- **Date**: {YYYY-MM-DD}
+- **Validation**: {validity answer}
+- **Scope**: {scope answer}
+- **Priority**: {priority answer}
+- **Changes**: {list of changes}
 ```
 
 ### Phase 6: Summary
@@ -345,13 +342,13 @@ Run `/levelup.implement` to:
 
 | File | Description |
 |------|-------------|
-| `{TEAM_DIRECTIVES}/.cdrs.json` | Updated Context Directive Records |
+| `{REPO_ROOT}/.specify/memory/cdr.md` | Updated Context Directive Records |
 
 ## Notes
 
-- Only modules with status "discovered" or "proposed" are clarified
-- Accepted modules (status "accepted") are ready for `/levelup.implement`
-- Rejected modules can be removed or kept with status "deprecated"
+- Only CDRs with status "Discovered" or "Proposed" are clarified
+- Accepted CDRs (status "Accepted") are ready for `/levelup.implement`
+- Rejected CDRs can be removed or kept with status "Deprecated"
 - Content can be revised multiple times before acceptance
 - No automatic handoff - user decides next step
 

extensions/levelup/commands/implement.md

@@ -25,15 +25,16 @@ You **MUST** consider the user input before proceeding (if not empty).
 Compile accepted CDRs into a **draft PR** to the team-ai-directives repository. Create or update context modules based on CDR decisions.
 
 **Input**:
-- Accepted CDRs from `{TEAM_DIRECTIVES}/.cdrs.json` (with status "accepted")
+- Accepted CDRs from `{REPO_ROOT}/.specify/memory/cdr.md` (with status "Accepted")
 - Draft skills from `.specify/drafts/skills/`
 - Team-ai-directives repository
 
 **Output**:
 - New branch in team-ai-directives
 - Created/updated context modules
 - Draft PR (or ready PR with `--ready` flag)
-- Updated CDR statuses to "active" in `.cdrs.json`
+- Creates/updates context modules in team-ai-directives
+- Copies accepted CDRs to `{TEAM_DIRECTIVES}/CDR.md`
 
 **MCP Integration**:
 
@@ -53,7 +54,7 @@ You are acting as a **Context Publisher** - moving accepted CDRs from local draf
 ### Prerequisites
 
 Before running:
-1. At least one module with status "accepted" in `{TEAM_DIRECTIVES}/.cdrs.json`
+1. At least one CDR with status "Accepted" in `{REPO_ROOT}/.specify/memory/cdr.md`
 2. Team-ai-directives repository configured and accessible
 3. Working tree at team-ai-directives is clean
 4. Git credentials configured for push
@@ -109,7 +110,7 @@ Please commit or stash changes before running /levelup.implement.
 
 #### Step 3: Load Accepted CDRs
 
-Read `{TEAM_DIRECTIVES}/.cdrs.json` and filter modules with:
+Read `{REPO_ROOT}/.specify/memory/cdr.md` and filter CDRs with:
 - Status = "accepted"
 
 If no accepted modules, **STOP**:
@@ -205,15 +206,69 @@ Update `.skills.json`:
 ```json
 {
   "skills": {
-    "internal": {
-      "local:./skills/{skill-name}": {
-        // entry from .skills-entry.json
-      }
+    "local:./skills/{skill-name}": {
+      "version": "1.0.0",
+      "description": "{description}"
     }
   }
 }
 ```
 
+#### Step 5: Extract Accepted CDRs to CDR.md
+
+Extract only CDRs with status "Accepted" from `{REPO_ROOT}/.specify/memory/cdr.md` and create `{TEAM_DIRECTIVES}/CDR.md`:
+
+1. Parse the source cdr.md file
+2. Filter to only include CDRs with status "Accepted"
+3. Generate new CDR.md with the accepted CDRs only
+
+```markdown
+# Context Directive Records
+
+Context Directive Records tracking approved contributions to team-ai-directives.
+
+## CDR Index
+
+| ID | Target Module | Context Type | Status | Date | Source |
+|----|---------------|--------------|--------|------|--------|
+| CDR-001 | context_modules/rules/python/error-handling.md | Rule | Accepted | 2026-03-12 | {project-name} |
+
+---
+
+## CDR-001: {Title}
+
+### Status
+
+**Accepted** | Proposed | Rejected
+
+### Date
+
+YYYY-MM-DD
+
+### Source
+
+{project-name}
+
+### Target Module
+
+`context_modules/rules/{domain}/{file}.md`
+
+### Context Type
+
+Rule | Persona | Example | Constitution Amendment
+
+### Context
+
+{Content from CDR}
+
+### Decision
+
+{Decision from CDR}
+
+...
+
+```
+
 ### Phase 3: Commit Changes
 
 **Objective**: Stage and commit all changes
@@ -222,7 +277,7 @@ Update `.skills.json`:
 
 ```bash
 cd "$TEAM_DIRECTIVES"
-git add context_modules/ skills/ .skills.json
+git add context_modules/ skills/ .skills.json CDR.md
 ```
 
 #### Step 2: Generate Commit Message
@@ -270,6 +325,10 @@ Context module contributions from **{project-name}**.
 | CDR-001 | Rule | context_modules/rules/python/error-handling.md |
 | CDR-002 | Example | context_modules/examples/testing/fixtures.md |
 
+### CDR Records
+
+Accepted CDRs are recorded in `CDR.md` for tracking.
+
 ### Skills Added
 
 - `{skill-name}`: {description}
@@ -323,35 +382,9 @@ MCP tools not available. Create PR manually:
 5. Body: {copy PR description above}
 ```
 
-### Phase 5: Update CDR Statuses
-
-**Objective**: Mark CDRs as active
+### Phase 5: Summary
 
-Update `{TEAM_DIRECTIVES}/.cdrs.json`:
-
-For each implemented module:
-- Change status: "accepted" → "active"
-
-Add implementation metadata to the module entry:
-```json
-{
-  "modules": {
-    "{module-id}": {
-      "path": "context_modules/rules/{domain}/{file}.md",
-      "type": "rule",
-      "status": "active",
-      "implemented": {
-        "date": "2026-03-12",
-        "branch": "{BRANCH_NAME}",
-        "pr": "{PR-URL}",
-        "commit": "{commit-sha}"
-      }
-    }
-  }
-}
-```
-
-### Phase 6: Summary
+**Objective**: Present implementation results
 
 **Objective**: Present implementation results
 
@@ -405,7 +438,7 @@ Add implementation metadata to the module entry:
 
 | File | Description |
 |------|-------------|
-| `{TEAM_DIRECTIVES}/.cdrs.json` | Updated CDR statuses (accepted → active) |
+| `{TEAM_DIRECTIVES}/CDR.md` | Accepted CDRs from this contribution |
 | `{TEAM_DIRECTIVES}/context_modules/**` | New/updated context modules |
 | `{TEAM_DIRECTIVES}/skills/**` | New skills |
 | `{TEAM_DIRECTIVES}/.skills.json` | Updated manifest |
@@ -420,8 +453,8 @@ Add implementation metadata to the module entry:
 ## Notes
 
 - Creates draft PR by default for review before merge
-- Only implements modules with status "accepted" in `.cdrs.json`
-- Updates module statuses to "active" after successful PR creation
+- Only implements CDRs with status "Accepted" from `.specify/memory/cdr.md`
+- Copies only accepted CDRs to `{TEAM_DIRECTIVES}/CDR.md`
 - Skills from `.specify/drafts/skills/` are included unless `--skip-skills`
 - If MCP unavailable, provides manual instructions
 - Working tree must be clean before running

extensions/levelup/commands/init.md

@@ -45,7 +45,7 @@ Scan an **existing codebase** (brownfield) and discover patterns that could beco
 
 **Output**:
 
-1. **Proposed modules** added to `{TEAM_DIRECTIVES}/.cdrs.json` with status "proposed"
+1. **Proposed modules** added to `{REPO_ROOT}/.specify/memory/cdr.md` with status "Discovered" or "Proposed"
 2. **Summary** of discovered patterns by context type
 3. **Manual handoff options** to `/levelup.clarify` or `/levelup.specify`
 
@@ -99,7 +99,7 @@ You are acting as a **Context Archaeologist** uncovering implicit team AI direct
 7. **Deduplication** (Phase 7): Filter out patterns already in team-ai-directives
 8. **CDR Generation** (Phase 8): Create CDRs for discovered patterns (status: "proposed")
 9. **Gap Analysis** (Phase 9): Identify areas where patterns are unclear
-10. **Output** (Phase 10): Write modules to `{TEAM_DIRECTIVES}/.cdrs.json`
+10. **Output** (Phase 10): Write CDRs to `{REPO_ROOT}/.specify/memory/cdr.md`
 11. **Handoff Options** (Phase 11): Present next step options
 
 ## Execution Steps
@@ -233,7 +233,7 @@ Run `{SCRIPT}` to set up the infrastructure:
 - Creates skills drafts directory at `.specify/drafts/skills/`
 - Returns JSON with `TEAM_DIRECTIVES`, `REPO_ROOT`
 
-The `.cdrs.json` file should already exist in team-ai-directives.
+The `.specify/memory/cdr.md` file will be created in the project directory.
 
 #### Step 2: Setup Directories
 
@@ -436,12 +436,12 @@ Document gaps for `/levelup.clarify`:
 
 #### Step 1: Write CDRs
 
-Add proposed modules to `{TEAM_DIRECTIVES}/.cdrs.json`:
+Add proposed CDRs to `{REPO_ROOT}/.specify/memory/cdr.md`:
 
-- Load existing `.cdrs.json`
-- Add new proposed modules with unique IDs
-- Save updated JSON
-- Do not overwrite existing active/accepted modules
+- Create `.specify/memory/` directory if it doesn't exist
+- Use the CDR template format (markdown with CDR index table)
+- Add new CDRs with unique IDs (CDR-001, CDR-002, etc.)
+- Do not overwrite existing accepted/active CDRs
 
 #### Step 2: Create Summary
 
@@ -480,9 +480,9 @@ Present discovery summary:
 
 ### Next Steps
 
-1. Review proposed modules in `{TEAM_DIRECTIVES}/.cdrs.json`
+1. Review proposed CDRs in `{REPO_ROOT}/.specify/memory/cdr.md`
 2. Run `/levelup.clarify` to resolve ambiguities
-3. Mark modules as "accepted" or "deprecated"
+3. Mark CDRs as "Accepted" or "Rejected"
 4. Run `/levelup.implement` to create PR
 ```
 
@@ -518,7 +518,7 @@ Run `/levelup.implement` to:
 
 | File | Description |
 |------|-------------|
-| `{TEAM_DIRECTIVES}/.cdrs.json` | Context Directive Records |
+| `{REPO_ROOT}/.specify/memory/cdr.md` | Context Directive Records (markdown) |
 
 ## Notes