agileflow 2.44.0 → 2.46.0

package/src/core/commands/diagnose.md

@@ -4,14 +4,6 @@ description: System health diagnostics
 
 # diagnose
 
-<!-- STEP 0: ACTIVATION -->
-<function_calls>
-<invoke name="Bash">
-<parameter name="command">node /home/coder/AgileFlow/scripts/activate-command.js diagnose</parameter>
-<parameter name="description">Activate diagnose command and show compact summary</parameter>
-</invoke>
-</function_calls>
-
 Run comprehensive AgileFlow system health checks to identify potential issues before they cause failures.
 
 ## Prompt
@@ -250,9 +242,9 @@ else
   echo "⚠️  Found $JSON_ERRORS issue(s) that need attention."
   echo ""
   echo "Next steps:"
-  echo "1. Fix JSON validation errors using: bash scripts/validate-json.sh <file>"
+  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 7"
+  echo "3. Run archival if status.json is too large: bash scripts/archive-completed-stories.sh"
   echo "4. Re-run diagnostics after fixes: /agileflow:diagnose"
   exit 1
 fi

package/src/core/commands/help.md

@@ -21,7 +21,7 @@ node scripts/obtain-context.js help
 **PURPOSE**: Immediately load full context before executing any logic.
 
 **ACTIONS**:
-1. Read `/home/coder/AgileFlow/packages/cli/src/core/commands/help.md` (this file) in its entirety
+1. Read this command file (`.agileflow/commands/help.md`) in its entirety
 2. Absorb all instructions, rules, and examples
 3. Proceed to execution phase with complete context
 

package/src/core/commands/packages.md

@@ -21,7 +21,7 @@ node scripts/obtain-context.js packages
 **PURPOSE**: Immediately load full context before executing any logic.
 
 **ACTIONS**:
-1. Read `/home/coder/AgileFlow/packages/cli/src/core/commands/packages.md` (this file) in its entirety
+1. Read this command file (`.agileflow/commands/packages.md`) in its entirety
 2. Absorb all instructions, rules, and examples
 3. Proceed to execution phase with complete context
 

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

@@ -22,7 +22,7 @@ node scripts/obtain-context.js readme-sync
 **PURPOSE**: Immediately load full context before executing any logic.
 
 **ACTIONS**:
-1. Read `/home/coder/AgileFlow/packages/cli/src/core/commands/readme-sync.md` (this file) in its entirety
+1. Read this command file (`.agileflow/commands/readme-sync.md`) in its entirety
 2. Absorb all instructions, rules, and examples
 3. Proceed to execution phase with complete context
 

package/src/core/commands/research.md

@@ -21,7 +21,7 @@ node scripts/obtain-context.js research
 **PURPOSE**: Immediately load full context before executing any logic.
 
 **ACTIONS**:
-1. Read `/home/coder/AgileFlow/packages/cli/src/core/commands/research.md` (this file) in its entirety
+1. Read this command file (`.agileflow/commands/research.md`) in its entirety
 2. Absorb all instructions, rules, and examples
 3. Proceed to execution phase with complete context
 

package/src/core/commands/status.md

@@ -24,7 +24,7 @@ This gathers git status, stories/epics, session state, and registers for PreComp
 **PURPOSE**: Immediately load full context before executing any logic.
 
 **ACTIONS**:
-1. Read `/home/coder/AgileFlow/packages/cli/src/core/commands/status.md` (this file) in its entirety
+1. Read this command file (`.agileflow/commands/status.md`) in its entirety
 2. Absorb all instructions, rules, and examples
 3. Proceed to execution phase with complete context
 
@@ -48,7 +48,7 @@ This gathers git status, stories/epics, session state, and registers for PreComp
 - **Backup**: Restore from docs/09-agents/status.json.backup if validation fails
 - **Output**: Diff-first, then YES/NO confirmation
 - **Critical**: User text automatically escaped by jq
-- **Related**: docs/09-agents/status.json, bus/log.jsonl, scripts/validate-json.sh
+- **Related**: docs/09-agents/status.json, bus/log.jsonl
 <!-- COMPACT_SUMMARY_END -->
 
 ---
@@ -69,7 +69,7 @@ ACTIONS
    # Validate status.json after modification
    if ! jq empty docs/09-agents/status.json 2>/dev/null; then
      echo "❌ ERROR: status.json is now invalid JSON after update!"
-     echo "Run: bash scripts/validate-json.sh docs/09-agents/status.json"
+     echo "Fix: Use jq to validate and repair the JSON structure"
      exit 1
    fi
    ```

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

@@ -22,7 +22,7 @@ node scripts/obtain-context.js story-validate
 **PURPOSE**: Immediately load full context before executing any logic.
 
 **ACTIONS**:
-1. Read `/home/coder/AgileFlow/packages/cli/src/core/commands/story-validate.md` (this file) in its entirety
+1. Read this command file (`.agileflow/commands/story-validate.md`) in its entirety
 2. Absorb all instructions, rules, and examples
 3. Proceed to execution phase with complete context
 

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

@@ -155,10 +155,10 @@ EXECUTION
 Run the validation script:
 ```bash
 # All domains
-bash .agileflow/scripts/validate-expertise.sh
+bash scripts/validate-expertise.sh
 
 # Specific domain
-bash .agileflow/scripts/validate-expertise.sh database
+bash scripts/validate-expertise.sh database
 ```
 
 Or manually check using Read tool on expertise files in:

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

@@ -50,6 +50,22 @@ class Installer {
     this.packageRoot = getPackageRoot();
   }
 
+  /**
+   * Clean up existing content directories before installing.
+   * Removes agents/, commands/, skills/, templates/ but preserves _cfg/ and config.yaml.
+   * @param {string} agileflowDir - AgileFlow installation directory
+   */
+  async cleanup(agileflowDir) {
+    const dirsToRemove = ['agents', 'commands', 'skills', 'templates'];
+
+    for (const dir of dirsToRemove) {
+      const dirPath = path.join(agileflowDir, dir);
+      if (await fs.pathExists(dirPath)) {
+        await fs.remove(dirPath);
+      }
+    }
+  }
+
   /**
    * Install AgileFlow to a project
    * @param {Object} config - Installation configuration
@@ -91,10 +107,13 @@ class Installer {
         backupPath = await this.createBackup(agileflowDir, cfgDir, timestamp);
       }
 
-      const fileIndex = existingFileIndex || { schema: 1, files: {} };
-      if (!fileIndex.files || typeof fileIndex.files !== 'object') {
-        fileIndex.files = {};
-      }
+      // Clean up existing content directories to remove stale files
+      // This happens AFTER backup so we can restore if needed
+      spinner.text = 'Cleaning up old content...';
+      await this.cleanup(agileflowDir);
+
+      // Reset file index since we removed all content - start fresh
+      const fileIndex = { schema: 1, files: {} };
 
       const fileOps = {
         created: 0,
@@ -132,6 +151,10 @@ class Installer {
         });
       }
 
+      // Copy essential scripts to user's scripts/ directory
+      spinner.text = 'Installing scripts...';
+      await this.installScripts(directory, { force: effectiveForce });
+
       // Create config.yaml
       spinner.text = 'Creating configuration...';
       await this.createConfig(agileflowDir, userName, agileflowFolder, { force: effectiveForce });
@@ -575,6 +598,76 @@ class Installer {
     return counts;
   }
 
+  /**
+   * Install all scripts from packages/cli/scripts/ to user's project scripts/ directory
+   * Copies everything automatically - no manual list to maintain
+   * @param {string} directory - Project directory
+   * @param {Object} options - Installation options
+   * @param {boolean} options.force - Overwrite existing scripts
+   */
+  async installScripts(directory, options = {}) {
+    const { force = false } = options;
+    const scriptsSourceDir = path.join(this.packageRoot, 'scripts');
+    const scriptsDestDir = path.join(directory, 'scripts');
+
+    // Skip if source scripts directory doesn't exist
+    if (!(await fs.pathExists(scriptsSourceDir))) {
+      return;
+    }
+
+    // Ensure destination scripts directory exists
+    await fs.ensureDir(scriptsDestDir);
+
+    // Copy all scripts recursively
+    await this.copyScriptsRecursive(scriptsSourceDir, scriptsDestDir, force);
+  }
+
+  /**
+   * Recursively copy scripts from source to destination
+   * @param {string} srcDir - Source directory
+   * @param {string} destDir - Destination directory
+   * @param {boolean} force - Overwrite existing files
+   */
+  async copyScriptsRecursive(srcDir, destDir, force) {
+    const entries = await fs.readdir(srcDir, { withFileTypes: true });
+
+    for (const entry of entries) {
+      const srcPath = path.join(srcDir, entry.name);
+      const destPath = path.join(destDir, entry.name);
+
+      if (entry.isDirectory()) {
+        // Recursively copy subdirectories
+        await fs.ensureDir(destPath);
+        await this.copyScriptsRecursive(srcPath, destPath, force);
+      } else {
+        // Copy file
+        const destExists = await fs.pathExists(destPath);
+
+        // If destination exists and not forcing, check if identical
+        if (destExists && !force) {
+          const srcContent = await fs.readFile(srcPath);
+          const destContent = await fs.readFile(destPath);
+          if (srcContent.equals(destContent)) {
+            continue; // Identical, skip
+          }
+          // Different content but not forcing, skip to preserve user changes
+          continue;
+        }
+
+        // Copy the file
+        await fs.copy(srcPath, destPath);
+
+        // Make executable on Unix for shell scripts and JS files
+        if (process.platform !== 'win32') {
+          const ext = path.extname(entry.name).toLowerCase();
+          if (['.sh', '.js'].includes(ext)) {
+            await fs.chmod(destPath, 0o755);
+          }
+        }
+      }
+    }
+  }
+
   /**
    * Get installation status
    * @param {string} directory - Project directory