fix: add {SCRIPT} invocation to levelup commands for proper script execution

- Add Phase 0 (Environment Setup) to spec, clarify, skills, and implement commands
- Each command now properly invokes {SCRIPT} to get paths from setup-levelup.sh
- Remove obsolete levelup scripts from main scripts/ folder (now in extension)
- Use CDR_FILE, TEAM_DIRECTIVES, SKILLS_DRAFTS from script JSON output
- Extension is now fully self-contained with working script references

Author: kanfil

extensions/levelup/commands/clarify.md

@@ -67,13 +67,32 @@ You are acting as a **Context Validator** reviewing discovered patterns. Your ro
 
 ## Execution Steps
 
+### Phase 0: Environment Setup
+
+**Objective**: Initialize CDR infrastructure and resolve paths
+
+Run `{SCRIPT}` from repository root and parse JSON output:
+
+```json
+{
+  "REPO_ROOT": "/path/to/project",
+  "CDR_FILE": "/path/to/project/.specify/memory/cdr.md",
+  "TEAM_DIRECTIVES": "/path/to/team-ai-directives",
+  "TEAM_DIRECTIVES_EXISTS": true,
+  "SKILLS_DRAFTS": "/path/to/project/.specify/drafts/skills",
+  "BRANCH": "current-branch"
+}
+```
+
+**IMPORTANT**: Run this script only ONCE. Use the JSON output to get all paths.
+
 ### Phase 1: Load Current State
 
 **Objective**: Load CDRs and team-ai-directives for validation
 
 #### Step 1: Load CDRs
 
-Read `.specify/memory/cdr.md` and parse all CDRs.
+Read CDR_FILE (from script output) and parse all CDRs.
 
 Filter CDRs by status:
 - **Primary**: Status = "Discovered" or "Proposed"
@@ -83,7 +102,7 @@ If user specified specific CDR IDs, filter to those.
 
 #### Step 2: Load Team Directives
 
-Load existing team-ai-directives for comparison:
+If TEAM_DIRECTIVES_EXISTS is true, load existing team-ai-directives for comparison:
 - `context_modules/constitution.md`
 - `context_modules/rules/**/*.md`
 - `context_modules/personas/*.md`
@@ -219,7 +238,7 @@ If content needs revision:
 
 #### Step 1: Update CDR File
 
-For each clarified CDR:
+Update CDR_FILE (from script output) for each clarified CDR:
 
 1. Update status
 2. Update content if revised

extensions/levelup/commands/implement.md

@@ -60,33 +60,45 @@ Before running:
 
 ## Execution Steps
 
+### Phase 0: Environment Setup
+
+**Objective**: Initialize CDR infrastructure and resolve paths
+
+Run `{SCRIPT}` from repository root and parse JSON output:
+
+```json
+{
+  "REPO_ROOT": "/path/to/project",
+  "CDR_FILE": "/path/to/project/.specify/memory/cdr.md",
+  "TEAM_DIRECTIVES": "/path/to/team-ai-directives",
+  "TEAM_DIRECTIVES_EXISTS": true,
+  "SKILLS_DRAFTS": "/path/to/project/.specify/drafts/skills",
+  "BRANCH": "current-branch"
+}
+```
+
+**IMPORTANT**: Run this script only ONCE. Use the JSON output to get all paths.
+
 ### Phase 1: Validate Environment
 
 **Objective**: Ensure prerequisites are met
 
-#### Step 1: Resolve Team Directives Path
+#### Step 1: Verify Team Directives
 
-```bash
-TEAM_DIRECTIVES="${SPECIFY_TEAM_DIRECTIVES:-}"
-if [[ -z "$TEAM_DIRECTIVES" ]]; then
-    if [[ -d ".specify/team-ai-directives" ]]; then
-        TEAM_DIRECTIVES=".specify/team-ai-directives"
-    elif [[ -d ".specify/memory/team-ai-directives" ]]; then
-        TEAM_DIRECTIVES=".specify/memory/team-ai-directives"
-    fi
-fi
-```
+Check TEAM_DIRECTIVES_EXISTS from script output.
 
-If not found, **STOP**:
+If false, **STOP**:
 ```
 Team AI directives repository not found.
 Run: specify init --team-ai-directives <path-or-url>
 ```
 
 #### Step 2: Check Working Tree
 
+Use TEAM_DIRECTIVES from script output:
+
 ```bash
-cd "$TEAM_DIRECTIVES"
+cd "{TEAM_DIRECTIVES}"
 git status --porcelain
 ```
 
@@ -98,7 +110,7 @@ Please commit or stash changes before running /levelup.implement.
 
 #### Step 3: Load Accepted CDRs
 
-Read `.specify/memory/cdr.md` and filter:
+Read CDR_FILE (from script output) and filter:
 - Status = "Accepted"
 
 If no accepted CDRs, **STOP**:
@@ -181,13 +193,13 @@ CDR: {CDR-ID}
 
 #### Step 4: Process Draft Skills
 
-If `.specify/drafts/skills/` contains skills (and not `--skip-skills`):
+If SKILLS_DRAFTS (from script output) contains skills (and not `--skip-skills`):
 
 1. Copy skill directory to `{TEAM_DIRECTIVES}/skills/`
 2. Read `.skills-entry.json` and merge into `.skills.json`
 
 ```bash
-cp -r .specify/drafts/skills/{skill-name} "$TEAM_DIRECTIVES/skills/"
+cp -r {SKILLS_DRAFTS}/{skill-name} "{TEAM_DIRECTIVES}/skills/"
 ```
 
 Update `.skills.json`:
@@ -316,7 +328,7 @@ MCP tools not available. Create PR manually:
 
 **Objective**: Mark CDRs as implemented
 
-Update `.specify/memory/cdr.md`:
+Update CDR_FILE (from script output):
 
 For each implemented CDR:
 - Change status: "Accepted" → "Implemented"

extensions/levelup/commands/skills.md

@@ -85,6 +85,27 @@ Skills follow the team-ai-directives format:
 
 ## Execution Steps
 
+### Phase 0: Environment Setup
+
+**Objective**: Initialize CDR infrastructure and resolve paths
+
+Run `{SCRIPT}` from repository root and parse JSON output:
+
+```json
+{
+  "REPO_ROOT": "/path/to/project",
+  "CDR_FILE": "/path/to/project/.specify/memory/cdr.md",
+  "TEAM_DIRECTIVES": "/path/to/team-ai-directives",
+  "TEAM_DIRECTIVES_EXISTS": true,
+  "SKILLS_DRAFTS": "/path/to/project/.specify/drafts/skills",
+  "BRANCH": "current-branch"
+}
+```
+
+**IMPORTANT**: Run this script only ONCE. Use the JSON output to get all paths.
+
+Skills will be created in SKILLS_DRAFTS directory.
+
 ### Phase 1: Parse User Input
 
 **Objective**: Determine which skill to build
@@ -105,7 +126,7 @@ If input is ambiguous, ask for clarification.
 
 #### Step 1: Load CDRs
 
-Read `.specify/memory/cdr.md` and filter:
+Read CDR_FILE (from script output) and filter:
 - Status = "Accepted"
 - Context Type = "Skill" (primary) or related types
 
@@ -139,8 +160,10 @@ Proceed with these CDRs? (Y/N or specify different CDRs)
 
 #### Step 1: Create Directory
 
+Use SKILLS_DRAFTS from script output:
+
 ```bash
-mkdir -p .specify/drafts/skills/{skill-name}/references
+mkdir -p {SKILLS_DRAFTS}/{skill-name}/references
 ```
 
 #### Step 2: Generate SKILL.md

extensions/levelup/commands/spec.md

@@ -60,13 +60,34 @@ If no feature context available, the command will note this and provide limited
 
 ## Execution Steps
 
+### Phase 0: Environment Setup
+
+**Objective**: Initialize CDR infrastructure and resolve paths
+
+Run `{SCRIPT}` from repository root and parse JSON output:
+
+```json
+{
+  "REPO_ROOT": "/path/to/project",
+  "CDR_FILE": "/path/to/project/.specify/memory/cdr.md",
+  "TEAM_DIRECTIVES": "/path/to/team-ai-directives",
+  "TEAM_DIRECTIVES_EXISTS": true,
+  "SKILLS_DRAFTS": "/path/to/project/.specify/drafts/skills",
+  "BRANCH": "feature/001-user-auth"
+}
+```
+
+**IMPORTANT**: Run this script only ONCE. Use the JSON output to get all paths.
+
+If `TEAM_DIRECTIVES_EXISTS` is false, warn user but continue (CDR enrichment still works).
+
 ### Phase 1: Load Feature Context
 
 **Objective**: Load current feature artifacts
 
 #### Step 1: Detect Feature Branch
 
-Detect current feature from:
+Use BRANCH from script output, or detect from:
 1. Git branch name (e.g., `feature/001-user-auth`)
 2. `SPECIFY_FEATURE` environment variable
 3. User-provided feature name
@@ -89,7 +110,7 @@ If artifacts are missing, note which are unavailable.
 
 **Objective**: Load CDRs to refine
 
-Read `.specify/memory/cdr.md` and filter:
+Read CDR_FILE (from script output) and filter:
 - Status = "Discovered" or "Proposed"
 - Match user-specified CDR IDs if provided
 
@@ -162,7 +183,7 @@ Append evidence to CDR:
 
 **Objective**: Write enriched CDRs to file
 
-Update `.specify/memory/cdr.md` with:
+Update CDR_FILE (from script output) with:
 - Added evidence sections
 - Updated "Date" field
 - Note about enrichment source