agileflow 2.49.0 → 2.50.0

package/src/core/commands/babysit.md

@@ -27,7 +27,7 @@ End-to-end mentor for implementing features.
 **Before doing ANYTHING else, run the context script to gather all project state in one shot:**
 
 ```bash
-node scripts/obtain-context.js babysit
+node .agileflow/scripts/obtain-context.js babysit
 ```
 
 This single command gathers:
@@ -70,7 +70,7 @@ Keep this section under 150 lines - it contains the critical behavioral rules an
 ### TodoWrite Tracking
 
 **CRITICAL**: Track progress with TodoWrite tool. Typical workflow:
-1. Run context script (`node scripts/obtain-context.js babysit`)
+1. Run context script (`node .agileflow/scripts/obtain-context.js babysit`)
 2. Present suggestions using AskUserQuestion
 3. Read task-specific docs based on user's choice
 4. Plan implementation steps with file paths
@@ -145,7 +145,7 @@ ROLE: Babysitter (Mentor + Orchestrator)
 TODO LIST TRACKING
 **CRITICAL**: Immediately create a todo list using TodoWrite tool to track mentoring workflow:
 ```
-1. Run context script (node scripts/obtain-context.js babysit)
+1. Run context script (node .agileflow/scripts/obtain-context.js babysit)
 2. Present intelligent suggestions using AskUserQuestion
 3. Read task-specific docs (based on what user chooses)
 4. Validate story readiness and architecture context
@@ -173,7 +173,7 @@ GOAL
 **Run the context script IMMEDIATELY - DO NOT SKIP:**
 
 ```bash
-node scripts/obtain-context.js babysit
+node .agileflow/scripts/obtain-context.js babysit
 ```
 
 This single command gathers all essential context:

package/src/core/commands/baseline.md

@@ -10,7 +10,7 @@ Create a verified checkpoint representing a known-good state of the project.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js baseline
+node .agileflow/scripts/obtain-context.js baseline
 ```
 
 <!-- COMPACT_SUMMARY_START -->

package/src/core/commands/blockers.md

@@ -9,7 +9,7 @@ model: haiku
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js blockers
+node .agileflow/scripts/obtain-context.js blockers
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/board.md

@@ -10,7 +10,7 @@ Generate a visual kanban board from current story statuses.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js board
+node .agileflow/scripts/obtain-context.js board
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/compress.md

@@ -202,8 +202,8 @@ When user runs `/agileflow:compress`:
 - After major epic completion (many stories with verbose records)
 
 **Combine with archival**:
-1. First run archival to move old completed stories: `/agileflow:compress` → runs `bash scripts/archive-completed-stories.sh`
-2. If still too large, run compression: `/agileflow:compress` → runs `bash scripts/compress-status.sh`
+1. First run archival to move old completed stories: `/agileflow:compress` → runs `bash .agileflow/scripts/archive-completed-stories.sh`
+2. If still too large, run compression: `/agileflow:compress` → runs `bash .agileflow/scripts/compress-status.sh`
 3. Result: status.json under 25000 tokens
 
 ## Safety
@@ -224,7 +224,7 @@ When user runs `/agileflow:compress`:
 ## Implementation
 
 ```bash
-bash scripts/compress-status.sh
+bash .agileflow/scripts/compress-status.sh
 ```
 
 ## Related Commands
@@ -321,7 +321,7 @@ fi
 
 **Step 2: Run compression**
 ```bash
-bash scripts/compress-status.sh
+bash .agileflow/scripts/compress-status.sh
 ```
 
 **Step 3: Verify and advise**
@@ -346,14 +346,14 @@ if [ ! -f scripts/compress-status.sh ]; then
 fi
 
 # Run compression
-bash scripts/compress-status.sh
+bash .agileflow/scripts/compress-status.sh
 ```
 
 **If compression isn't enough**:
 ```bash
 # Combine with aggressive archival
-bash scripts/archive-completed-stories.sh 3  # Archive stories >3 days old
-bash scripts/compress-status.sh              # Then compress remaining
+bash .agileflow/scripts/archive-completed-stories.sh 3  # Archive stories >3 days old
+bash .agileflow/scripts/compress-status.sh              # Then compress remaining
 ```
 
 **Always**:

package/src/core/commands/configure.md

@@ -11,19 +11,19 @@ Configuration management with **profiles**, **enable/disable**, and **format mig
 
 ### Workflow (MUST FOLLOW)
 
-1. **Run detection**: `node scripts/agileflow-configure.js --detect`
+1. **Run detection**: `node .agileflow/scripts/agileflow-configure.js --detect`
 2. **If ⚠️ INVALID FORMAT shown**: Ask user to fix with `--migrate` BEFORE anything else
 3. **Present options**: Profiles, enable/disable, or check status
 
 ### Quick Commands
 
 ```bash
-node scripts/agileflow-configure.js --detect           # Check status
-node scripts/agileflow-configure.js --migrate          # Fix format issues
-node scripts/agileflow-configure.js --profile=full     # Enable all
-node scripts/agileflow-configure.js --profile=none     # Disable all
-node scripts/agileflow-configure.js --enable=stop      # Enable specific
-node scripts/agileflow-configure.js --disable=archival # Disable specific
+node .agileflow/scripts/agileflow-configure.js --detect           # Check status
+node .agileflow/scripts/agileflow-configure.js --migrate          # Fix format issues
+node .agileflow/scripts/agileflow-configure.js --profile=full     # Enable all
+node .agileflow/scripts/agileflow-configure.js --profile=none     # Disable all
+node .agileflow/scripts/agileflow-configure.js --enable=stop      # Enable specific
+node .agileflow/scripts/agileflow-configure.js --disable=archival # Disable specific
 ```
 
 ### Features
@@ -49,7 +49,7 @@ ROLE: Configuration Manager
 ## STEP 1: Always Run Detection First
 
 ```bash
-node scripts/agileflow-configure.js --detect
+node .agileflow/scripts/agileflow-configure.js --detect
 ```
 
 **CRITICAL**: Check the output for format issues (⚠️ INVALID FORMAT).
@@ -74,7 +74,7 @@ If you see `⚠️ INVALID FORMAT` in the detection output, **immediately ask us
 
 If user says yes:
 ```bash
-node scripts/agileflow-configure.js --migrate
+node .agileflow/scripts/agileflow-configure.js --migrate
 ```
 
 ## STEP 3: Configuration Options
@@ -104,32 +104,32 @@ After fixing issues (or if no issues), present main options:
 
 ```bash
 # Full - all features
-node scripts/agileflow-configure.js --profile=full
+node .agileflow/scripts/agileflow-configure.js --profile=full
 
 # Basic - essential hooks + archival
-node scripts/agileflow-configure.js --profile=basic
+node .agileflow/scripts/agileflow-configure.js --profile=basic
 
 # Minimal - welcome + archival
-node scripts/agileflow-configure.js --profile=minimal
+node .agileflow/scripts/agileflow-configure.js --profile=minimal
 
 # None - disable all AgileFlow features
-node scripts/agileflow-configure.js --profile=none
+node .agileflow/scripts/agileflow-configure.js --profile=none
 ```
 
 **Option B: Enable/disable specific features**
 
 ```bash
 # Enable features
-node scripts/agileflow-configure.js --enable=sessionstart,precompact,stop
+node .agileflow/scripts/agileflow-configure.js --enable=sessionstart,precompact,stop
 
 # Disable features
-node scripts/agileflow-configure.js --disable=statusline
+node .agileflow/scripts/agileflow-configure.js --disable=statusline
 
 # Both at once
-node scripts/agileflow-configure.js --enable=stop --disable=archival
+node .agileflow/scripts/agileflow-configure.js --enable=stop --disable=archival
 
 # With custom archival days
-node scripts/agileflow-configure.js --enable=archival --archival-days=14
+node .agileflow/scripts/agileflow-configure.js --enable=archival --archival-days=14
 ```
 
 ## Profile Details
@@ -198,19 +198,19 @@ The script handles these migrations automatically:
 **Hook string format:**
 ```json
 // OLD (invalid)
-"PreCompact": "./scripts/precompact-context.sh"
+"PreCompact": "./.agileflow/scripts/precompact-context.sh"
 
 // NEW (valid)
-"PreCompact": [{"matcher": "", "hooks": [{"type": "command", "command": "bash ./scripts/precompact-context.sh"}]}]
+"PreCompact": [{"matcher": "", "hooks": [{"type": "command", "command": "bash ./.agileflow/scripts/precompact-context.sh"}]}]
 ```
 
 **StatusLine missing type:**
 ```json
 // OLD (invalid)
-"statusLine": {"command": "./scripts/statusline.sh", "refreshInterval": 5000}
+"statusLine": {"command": "./.agileflow/scripts/statusline.sh", "refreshInterval": 5000}
 
 // NEW (valid)
-"statusLine": {"type": "command", "command": "./scripts/statusline.sh", "padding": 0}
+"statusLine": {"type": "command", "command": "./.agileflow/scripts/statusline.sh", "padding": 0}
 ```
 
 ## Metadata Tracking

package/src/core/commands/deps.md

@@ -13,7 +13,7 @@ Visualize and analyze story/epic dependency graphs with critical path analysis a
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js deps
+node .agileflow/scripts/obtain-context.js deps
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/diagnose.md

@@ -212,7 +212,7 @@ if [ -f docs/09-agents/status.json ]; then
   if [ $STATUS_SIZE -gt 102400 ]; then
     echo "  ⚠️  WARNING: status.json exceeds 100KB"
     echo "     Recommendation: Run archival to reduce file size"
-    echo "     Command: bash scripts/archive-completed-stories.sh 7"
+    echo "     Command: bash .agileflow/scripts/archive-completed-stories.sh 7"
   elif [ $STATUS_SIZE -gt 51200 ]; then
     echo "  ℹ️  status.json is getting large (>50KB)"
     echo "     Consider running archival soon"
@@ -244,7 +244,7 @@ else
   echo "Next steps:"
   echo "1. Fix JSON validation errors using: jq empty <file> to check, then repair manually"
   echo "2. Add missing files to .gitignore if needed"
-  echo "3. Run archival if status.json is too large: bash scripts/archive-completed-stories.sh"
+  echo "3. Run archival if status.json is too large: bash .agileflow/scripts/archive-completed-stories.sh"
   echo "4. Re-run diagnostics after fixes: /agileflow:diagnose"
   exit 1
 fi

package/src/core/commands/docs.md

@@ -12,7 +12,7 @@ Synchronize documentation with codebase changes.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js docs
+node .agileflow/scripts/obtain-context.js docs
 ```
 
 ---

package/src/core/commands/epic.md

@@ -10,7 +10,7 @@ argument-hint: EPIC=<EP-ID> TITLE=<text> OWNER=<id> GOAL=<text> [STORIES=<list>]
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js epic
+node .agileflow/scripts/obtain-context.js epic
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/help.md

@@ -11,7 +11,7 @@ Display a concise overview of the AgileFlow system.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js help
+node .agileflow/scripts/obtain-context.js help
 ```
 
 ---

package/src/core/commands/metrics.md

@@ -11,7 +11,7 @@ model: haiku
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js metrics
+node .agileflow/scripts/obtain-context.js metrics
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/packages.md

@@ -11,7 +11,7 @@ Manage project package dependencies (npm, pip, cargo, etc.) with dashboard, upda
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js packages
+node .agileflow/scripts/obtain-context.js packages
 ```
 
 ---

package/src/core/commands/pr.md

@@ -8,7 +8,7 @@ argument-hint: STORY=<US-ID> [TITLE=<text>] [TEST_EVIDENCE=<text>]
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js pr
+node .agileflow/scripts/obtain-context.js pr
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/readme-sync.md

@@ -12,7 +12,7 @@ Synchronize a folder's README.md with its current contents.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js readme-sync
+node .agileflow/scripts/obtain-context.js readme-sync
 ```
 
 ---

package/src/core/commands/research.md

@@ -11,7 +11,7 @@ Initialize or save research notes to the research folder.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js research
+node .agileflow/scripts/obtain-context.js research
 ```
 
 ---

package/src/core/commands/retro.md

@@ -11,7 +11,7 @@ model: haiku
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js retro
+node .agileflow/scripts/obtain-context.js retro
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/sprint.md

@@ -71,7 +71,7 @@ Intelligent sprint planning with capacity-based story selection, dependency vali
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js sprint
+node .agileflow/scripts/obtain-context.js sprint
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/status.md

@@ -12,7 +12,7 @@ Update story status and broadcast to agents via message bus.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js status
+node .agileflow/scripts/obtain-context.js status
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/story-validate.md

@@ -12,7 +12,7 @@ Validate a specific story for completeness, architecture context, and readiness
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js story-validate
+node .agileflow/scripts/obtain-context.js story-validate
 ```
 
 ---

package/src/core/commands/story.md

@@ -12,7 +12,7 @@ Create a new user story with acceptance criteria and test stubs.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js story
+node .agileflow/scripts/obtain-context.js story
 ```
 
 ---

package/src/core/commands/template.md

@@ -11,7 +11,7 @@ Create and manage custom templates for stories, epics, ADRs, and other documents
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js template
+node .agileflow/scripts/obtain-context.js template
 ```
 
 ---

package/src/core/commands/tests.md

@@ -11,7 +11,7 @@ Automatically set up testing infrastructure for projects without existing tests.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js tests
+node .agileflow/scripts/obtain-context.js tests
 ```
 
 ---

package/src/core/commands/update.md

@@ -11,7 +11,7 @@ Generate stakeholder communication updates from project status.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js update
+node .agileflow/scripts/obtain-context.js update
 ```
 
 ---

package/src/core/commands/validate-expertise.md

@@ -13,7 +13,7 @@ Validate agent expertise files to ensure they haven't drifted from the codebase.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js validate-expertise
+node .agileflow/scripts/obtain-context.js validate-expertise
 ```
 
 ---
@@ -155,10 +155,10 @@ EXECUTION
 Run the validation script:
 ```bash
 # All domains
-bash scripts/validate-expertise.sh
+bash .agileflow/scripts/validate-expertise.sh
 
 # Specific domain
-bash scripts/validate-expertise.sh database
+bash .agileflow/scripts/validate-expertise.sh database
 ```
 
 Or manually check using Read tool on expertise files in:

package/src/core/commands/velocity.md

@@ -12,7 +12,7 @@ Track team velocity, calculate trends, and forecast completion dates.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js velocity
+node .agileflow/scripts/obtain-context.js velocity
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/commands/verify.md

@@ -12,7 +12,7 @@ Execute project tests and update test status for stories.
 ## STEP 0: Gather Context
 
 ```bash
-node scripts/obtain-context.js verify
+node .agileflow/scripts/obtain-context.js verify
 ```
 
 This gathers git status, stories/epics, session state, and registers for PreCompact.

package/src/core/experts/devops/expertise.yaml

@@ -13,7 +13,7 @@ files:
         - "Commit and push to main"
         - "Create and push git tag v*.*.*"
         - "Create GitHub release with gh CLI"
-      usage: "./scripts/release.sh 2.32.0 'Feature Name'"
+      usage: "./.agileflow/scripts/release.sh 2.32.0 'Feature Name'"
 
   scripts:
     - path: scripts/agileflow-statusline.sh
@@ -63,7 +63,7 @@ relationships:
 patterns:
   - name: Automated Release
     description: "Use release.sh for all releases - never manual"
-    command: "./scripts/release.sh <version> 'Title'"
+    command: "./.agileflow/scripts/release.sh <version> 'Title'"
 
   - name: Version Sync
     description: "Version in 2 files: packages/cli/package.json and package.json"

package/src/core/experts/monitoring/expertise.yaml

@@ -145,7 +145,7 @@ learnings:
     context: "AgileFlow monitoring patterns"
     learning: |
       Session hooks run on SessionStart via .claude/settings.json hooks configuration.
-      The default SessionStart hook executes 'node scripts/get-env.js' to display
+      The default SessionStart hook executes 'node .agileflow/scripts/get-env.js' to display
       project info, git status, and system details at session start. This provides
       immediate context about the development environment.
 

package/src/core/templates/agileflow-configure.js

@@ -11,7 +11,7 @@
  *   - RECONFIGURE: Change settings (archival days, etc.)
  *
  * Usage:
- *   node scripts/agileflow-configure.js [options]
+ *   node .agileflow/scripts/agileflow-configure.js [options]
  *
  * Options:
  *   --profile=full|basic|minimal|none   Apply a preset
@@ -476,7 +476,7 @@ CHANGES=$(git status --porcelain 2>/dev/null | wc -l | tr -d ' ')
       if (!hasArchival) {
         settings.hooks.SessionStart[0].hooks.push({
           type: 'command',
-          command: 'bash scripts/archive-completed-stories.sh --quiet'
+          command: 'bash .agileflow/scripts/archive-completed-stories.sh --quiet'
         });
       }
     }
@@ -504,7 +504,7 @@ echo "[$MODEL] AgileFlow"
 
     settings.statusLine = {
       type: 'command',
-      command: 'bash scripts/agileflow-statusline.sh',
+      command: 'bash .agileflow/scripts/agileflow-statusline.sh',
       padding: 0
     };
     success('Status line enabled');
@@ -765,7 +765,7 @@ function printHelp() {
 ${c.bold}AgileFlow Configure${c.reset} - Manage AgileFlow features
 
 ${c.cyan}Usage:${c.reset}
-  node scripts/agileflow-configure.js [options]
+  node .agileflow/scripts/agileflow-configure.js [options]
 
 ${c.cyan}Profiles:${c.reset}
   --profile=full      All features (hooks, archival, statusline)
@@ -796,28 +796,28 @@ ${c.cyan}Maintenance:${c.reset}
 
 ${c.cyan}Examples:${c.reset}
   # Quick setup with all features
-  node scripts/agileflow-configure.js --profile=full
+  node .agileflow/scripts/agileflow-configure.js --profile=full
 
   # Enable specific features
-  node scripts/agileflow-configure.js --enable=sessionstart,precompact,stop
+  node .agileflow/scripts/agileflow-configure.js --enable=sessionstart,precompact,stop
 
   # Disable a feature
-  node scripts/agileflow-configure.js --disable=statusline
+  node .agileflow/scripts/agileflow-configure.js --disable=statusline
 
   # Show only agileflow branding and context in statusline
-  node scripts/agileflow-configure.js --hide=model,story,epic,wip,cost,git
+  node .agileflow/scripts/agileflow-configure.js --hide=model,story,epic,wip,cost,git
 
   # Re-enable git branch in statusline
-  node scripts/agileflow-configure.js --show=git
+  node .agileflow/scripts/agileflow-configure.js --show=git
 
   # List component status
-  node scripts/agileflow-configure.js --components
+  node .agileflow/scripts/agileflow-configure.js --components
 
   # Fix format issues
-  node scripts/agileflow-configure.js --migrate
+  node .agileflow/scripts/agileflow-configure.js --migrate
 
   # Check current status
-  node scripts/agileflow-configure.js --detect
+  node .agileflow/scripts/agileflow-configure.js --detect
 `);
 }
 

package/src/core/templates/agileflow-welcome.js

@@ -152,7 +152,7 @@ function runArchival(rootDir) {
     if (toArchiveCount > 0) {
       // Run archival
       try {
-        execSync('bash scripts/archive-completed-stories.sh', {
+        execSync('bash .agileflow/scripts/archive-completed-stories.sh', {
           cwd: rootDir,
           encoding: 'utf8',
           stdio: 'pipe'

package/src/core/templates/claude-settings.advanced.example.json

@@ -10,11 +10,11 @@
           },
           {
             "type": "command",
-            "command": "echo '📁 Project: $(node scripts/get-env.js PROJECT_NAME \"Unnamed Project\")'"
+            "command": "echo '📁 Project: $(node .agileflow/scripts/get-env.js PROJECT_NAME \"Unnamed Project\")'"
           },
           {
             "type": "command",
-            "command": "echo '👤 Developer: $(node scripts/get-env.js USER_NAME \"Developer\")'"
+            "command": "echo '👤 Developer: $(node .agileflow/scripts/get-env.js USER_NAME \"Developer\")'"
           },
           {
             "type": "command",

package/src/core/templates/claude-settings.example.json

@@ -15,7 +15,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "bash scripts/archive-completed-stories.sh > /dev/null 2>&1 &"
+            "command": "bash .agileflow/scripts/archive-completed-stories.sh > /dev/null 2>&1 &"
           }
         ]
       }

package/tools/cli/installers/core/installer.js

@@ -599,7 +599,7 @@ class Installer {
   }
 
   /**
-   * Install all scripts from packages/cli/scripts/ to user's project scripts/ directory
+   * Install all scripts from packages/cli/scripts/ to .agileflow/scripts/
    * Copies everything automatically - no manual list to maintain
    * @param {string} directory - Project directory
    * @param {Object} options - Installation options
@@ -608,7 +608,7 @@ class Installer {
   async installScripts(directory, options = {}) {
     const { force = false } = options;
     const scriptsSourceDir = path.join(this.packageRoot, 'scripts');
-    const scriptsDestDir = path.join(directory, 'scripts');
+    const scriptsDestDir = path.join(directory, '.agileflow', 'scripts');
 
     // Skip if source scripts directory doesn't exist
     if (!(await fs.pathExists(scriptsSourceDir))) {