Merge pull request #563 from danwashusen/plan-project-structure-fix

Refined wording in `plan-template.md` to ensure the Source Code section consistently works

.github/workflows/scripts/create-github-release.sh

@@ -36,5 +36,7 @@ gh release create "$VERSION" \
   .genreleases/spec-kit-template-kilocode-ps-"$VERSION".zip \
   .genreleases/spec-kit-template-auggie-sh-"$VERSION".zip \
   .genreleases/spec-kit-template-auggie-ps-"$VERSION".zip \
+  .genreleases/spec-kit-template-roo-sh-"$VERSION".zip \
+  .genreleases/spec-kit-template-roo-ps-"$VERSION".zip \
   --title "Spec Kit Templates - $VERSION_NO_V" \
   --notes-file release_notes.md

.github/workflows/scripts/create-release-packages.sh

@@ -169,13 +169,16 @@ build_variant() {
     auggie)
       mkdir -p "$base_dir/.augment/commands"
       generate_commands auggie md "\$ARGUMENTS" "$base_dir/.augment/commands" "$script" ;;
+    roo)
+      mkdir -p "$base_dir/.roo/commands"
+      generate_commands roo md "\$ARGUMENTS" "$base_dir/.roo/commands" "$script" ;;
   esac
   ( cd "$base_dir" && zip -r "../spec-kit-template-${agent}-${script}-${NEW_VERSION}.zip" . )
   echo "Created $GENRELEASES_DIR/spec-kit-template-${agent}-${script}-${NEW_VERSION}.zip"
 }
 
 # Determine agent list
-ALL_AGENTS=(claude gemini copilot cursor qwen opencode windsurf codex kilocode auggie)
+ALL_AGENTS=(claude gemini copilot cursor qwen opencode windsurf codex kilocode auggie roo)
 ALL_SCRIPTS=(sh ps)
 
 

CHANGELOG.md

@@ -1,10 +1,32 @@
 # Changelog
 
+<!-- markdownlint-disable MD024 -->
+
 All notable changes to the Specify CLI will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.0.17] - 2025-09-22
+
+### Added
+
+- New `/clarify` command template to surface up to 5 targeted clarification questions for an existing spec and persist answers into a Clarifications section in the spec.
+- New `/analyze` command template providing a non-destructive cross-artifact discrepancy and alignment report (spec, clarifications, plan, tasks, constitution) inserted after `/tasks` and before `/implement`.
+	- Note: Constitution rules are explicitly treated as non-negotiable; any conflict is a CRITICAL finding requiring artifact remediation, not weakening of principles.
+
+## [0.0.16] - 2025-09-22
+
+### Added
+
+- `--force` flag for `init` command to bypass confirmation when using `--here` in a non-empty directory and proceed with merging/overwriting files.
+
+## [0.0.15] - 2025-09-21
+
+### Added
+
+- Support for Roo Code.
+
 ## [0.0.14] - 2025-09-21
 
 ### Changed

CONTRIBUTING.md

@@ -47,12 +47,40 @@ When working on spec-kit:
 
 ## AI contributions in Spec Kit
 
+> [!IMPORTANT]
+>
+> If you are using **any kind of AI assistance** to contribute to Spec Kit,
+> it must be disclosed in the pull request or issue.
+
 We welcome and encourage the use of AI tools to help improve Spec Kit! Many valuable contributions have been enhanced with AI assistance for code generation, issue detection, and feature definition.
 
+That being said, if you are using any kind of AI assistance (e.g., agents, ChatGPT) while contributing to Spec Kit,
+**this must be disclosed in the pull request or issue**, along with the extent to which AI assistance was used (e.g., documentation comments vs. code generation).
+
+If your PR responses or comments are being generated by an AI, disclose that as well.
+
+As an exception, trivial spacing or typo fixes don't need to be disclosed, so long as the changes are limited to small parts of the code or short phrases.
+
+An example disclosure:
+
+> This PR was written primarily by GitHub Copilot.
+
+Or a more detailed disclosure:
+
+> I consulted ChatGPT to understand the codebase but the solution
+> was fully authored manually by myself.
+
+Failure to disclose this is first and foremost rude to the human operators on the other end of the pull request, but it also makes it difficult to
+determine how much scrutiny to apply to the contribution.
+
+In a perfect world, AI assistance would produce equal or higher quality work than any human. That isn't the world we live in today, and in most cases
+where human supervision or expertise is not in the loop, it's generating code that cannot be reasonably maintained or evolved.
+
 ### What we're looking for
 
 When submitting AI-assisted contributions, please ensure they include:
 
+- **Clear disclosure of AI use** - You are transparent about AI use and degree to which you're using it for the contribution
 - **Human understanding and testing** - You've personally tested the changes and understand what they do
 - **Clear rationale** - You can explain why the change is needed and how it fits within Spec Kit's goals  
 - **Concrete evidence** - Include test cases, scenarios, or examples that demonstrate the improvement
@@ -72,6 +100,8 @@ The key is demonstrating that you understand and have validated your proposed ch
 
 Contributors who consistently submit low-effort AI-generated changes may be restricted from further contributions at the maintainers' discretion.
 
+Please be respectful to maintainers and disclose AI assistance.
+
 ## Resources
 
 - [Spec-Driven Development Methodology](./spec-driven.md)

README.md

@@ -39,12 +39,38 @@ Spec-Driven Development **flips the script** on traditional software development
 
 ### 1. Install Specify
 
-Initialize your project depending on the coding agent you're using:
+Choose your preferred installation method:
+
+#### Option 1: Persistent Installation (Recommended)
+
+Install once and use everywhere:
+
+```bash
+uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
+```
+
+Then use the tool directly:
+
+```bash
+specify init <PROJECT_NAME>
+specify check
+```
+
+#### Option 2: One-time Usage
+
+Run directly without installing:
 
 ```bash
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
 ```
 
+**Benefits of persistent installation:**
+
+- Tool stays installed and available in PATH
+- No need to create shell aliases
+- Better tool management with `uv tool list`, `uv tool upgrade`, `uv tool uninstall`
+- Cleaner shell configuration
+
 ### 2. Establish project principles
 
 Use the **`/constitution`** command to create your project's governing principles and development guidelines that will guide all subsequent development.
@@ -106,6 +132,7 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 | [Windsurf](https://windsurf.com/)                         | ✅ |                                                   |
 | [Kilo Code](https://github.com/Kilo-Org/kilocode)         | ✅ |                                                   |
 | [Auggie CLI](https://docs.augmentcode.com/cli/overview)   | ✅ |                                                   |
+| [Roo Code](https://roocode.com/)                          | ✅ |                                                   |
 | [Codex CLI](https://github.com/openai/codex)              | ⚠️ | Codex [does not support](https://github.com/openai/codex/issues/2890) custom arguments for slash commands.  |
 
 ## 🔧 Specify CLI Reference
@@ -124,11 +151,12 @@ The `specify` command supports the following options:
 | Argument/Option        | Type     | Description                                                                  |
 |------------------------|----------|------------------------------------------------------------------------------|
 | `<project-name>`       | Argument | Name for your new project directory (optional if using `--here`)            |
-| `--ai`                 | Option   | AI assistant to use: `claude`, `gemini`, `copilot`, `cursor`, `qwen`, `opencode`, `codex`, `windsurf`, `kilocode`, or `auggie` |
+| `--ai`                 | Option   | AI assistant to use: `claude`, `gemini`, `copilot`, `cursor`, `qwen`, `opencode`, `codex`, `windsurf`, `kilocode`, `auggie`, or `roo` |
 | `--script`             | Option   | Script variant to use: `sh` (bash/zsh) or `ps` (PowerShell)                 |
 | `--ignore-agent-tools` | Flag     | Skip checks for AI agent tools like Claude Code                             |
 | `--no-git`             | Flag     | Skip git repository initialization                                          |
 | `--here`               | Flag     | Initialize project in the current directory instead of creating a new one   |
+| `--force`              | Flag     | Force merge/overwrite when using `--here` in a non-empty directory (skip confirmation) |
 | `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                 |
 | `--debug`              | Flag     | Enable detailed debug output for troubleshooting                            |
 | `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)  |
@@ -154,6 +182,9 @@ specify init my-project --ai copilot --script ps
 # Initialize in current directory
 specify init --here --ai copilot
 
+# Force merge into current (non-empty) directory without confirmation
+specify init --here --force --ai copilot
+
 # Skip git initialization
 specify init my-project --ai gemini --no-git
 
@@ -175,8 +206,10 @@ After running `specify init`, your AI coding agent will have access to these sla
 |-----------------|-----------------------------------------------------------------------|
 | `/constitution` | Create or update project governing principles and development guidelines |
 | `/specify`      | Define what you want to build (requirements and user stories)        |
+| `/clarify`      | Clarify underspecified areas (must be run before `/plan` unless explicitly skipped; formerly `/quizme`) |
 | `/plan`         | Create technical implementation plans with your chosen tech stack     |
 | `/tasks`        | Generate actionable task lists for implementation                     |
+| `/analyze`      | Cross-artifact consistency & coverage analysis (run after /tasks, before /implement) |
 | `/implement`    | Execute all tasks to build the feature according to the plan         |
 
 ### Environment Variables
@@ -260,6 +293,8 @@ Or initialize in the current directory:
 
 ```bash
 specify init --here
+# Skip confirmation when the directory already has files
+specify init --here --force
 ```
 
 ![Specify CLI bootstrapping a new project in the terminal](./media/specify_cli.gif)
@@ -278,6 +313,8 @@ specify init <project_name> --ai windsurf
 # Or in current directory:
 specify init --here --ai claude
 specify init --here --ai codex
+# Force merge into a non-empty current directory
+specify init --here --force --ai claude
 ```
 
 The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, or Codex CLI installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
@@ -340,8 +377,7 @@ At this stage, your project folder contents should resemble the following:
 
 ```text
 ├── memory
-│	 ├── constitution.md
-│	 └── constitution_update_checklist.md
+│	 └── constitution.md
 ├── scripts
 │	 ├── check-prerequisites.sh
 │	 ├── common.sh
@@ -357,9 +393,19 @@ At this stage, your project folder contents should resemble the following:
     └── tasks-template.md
 ```
 
-### **STEP 3:** Functional specification clarification
+### **STEP 3:** Functional specification clarification (required before planning)
 
-With the baseline specification created, you can go ahead and clarify any of the requirements that were not captured properly within the first shot attempt. For example, you could use a prompt like this within the same Claude Code session:
+With the baseline specification created, you can go ahead and clarify any of the requirements that were not captured properly within the first shot attempt.
+
+You should run the structured clarification workflow **before** creating a technical plan to reduce rework downstream.
+
+Preferred order:
+1. Use `/clarify` (structured) – sequential, coverage-based questioning that records answers in a Clarifications section.
+2. Optionally follow up with ad-hoc free-form refinement if something still feels vague.
+
+If you intentionally want to skip clarification (e.g., spike or exploratory prototype), explicitly state that so the agent doesn't block on missing clarifications.
+
+Example free-form refinement prompt (after `/clarify` if still needed):
 
 ```text
 For each sample project or project that you create there should be a variable number of tasks between 5 and 15
@@ -391,8 +437,7 @@ The output of this step will include a number of implementation detail documents
 .
 ├── CLAUDE.md
 ├── memory
-│	 ├── constitution.md
-│	 └── constitution_update_checklist.md
+│	 └── constitution.md
 ├── scripts
 │	 ├── check-prerequisites.sh
 │	 ├── common.sh

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.0.14"
+version = "0.0.17"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [

scripts/bash/check-prerequisites.sh

@@ -82,14 +82,20 @@ source "$SCRIPT_DIR/common.sh"
 eval $(get_feature_paths)
 check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 
-# If paths-only mode, output paths and exit
+# If paths-only mode, output paths and exit (support JSON + paths-only combined)
 if $PATHS_ONLY; then
-    echo "REPO_ROOT: $REPO_ROOT"
-    echo "BRANCH: $CURRENT_BRANCH"
-    echo "FEATURE_DIR: $FEATURE_DIR"
-    echo "FEATURE_SPEC: $FEATURE_SPEC"
-    echo "IMPL_PLAN: $IMPL_PLAN"
-    echo "TASKS: $TASKS"
+    if $JSON_MODE; then
+        # Minimal JSON paths payload (no validation performed)
+        printf '{"REPO_ROOT":"%s","BRANCH":"%s","FEATURE_DIR":"%s","FEATURE_SPEC":"%s","IMPL_PLAN":"%s","TASKS":"%s"}\n' \
+            "$REPO_ROOT" "$CURRENT_BRANCH" "$FEATURE_DIR" "$FEATURE_SPEC" "$IMPL_PLAN" "$TASKS"
+    else
+        echo "REPO_ROOT: $REPO_ROOT"
+        echo "BRANCH: $CURRENT_BRANCH"
+        echo "FEATURE_DIR: $FEATURE_DIR"
+        echo "FEATURE_SPEC: $FEATURE_SPEC"
+        echo "IMPL_PLAN: $IMPL_PLAN"
+        echo "TASKS: $TASKS"
+    fi
     exit 0
 fi
 

scripts/bash/create-new-feature.sh

@@ -80,7 +80,7 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"
 
-TEMPLATE="$REPO_ROOT/templates/spec-template.md"
+TEMPLATE="$REPO_ROOT/.specify/templates/spec-template.md"
 SPEC_FILE="$FEATURE_DIR/spec.md"
 if [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
 

scripts/bash/update-agent-context.sh

@@ -68,6 +68,7 @@ AGENTS_FILE="$REPO_ROOT/AGENTS.md"
 WINDSURF_FILE="$REPO_ROOT/.windsurf/rules/specify-rules.md"
 KILOCODE_FILE="$REPO_ROOT/.kilocode/rules/specify-rules.md"
 AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
+ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
 
 # Template file
 TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
@@ -576,9 +577,12 @@ update_specific_agent() {
         auggie)
             update_agent_file "$AUGGIE_FILE" "Auggie CLI"
             ;;
+        roo)
+            update_agent_file "$ROO_FILE" "Roo Code"
+            ;;
         *)
             log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie"
+            log_error "Expected: claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie|roo"
             exit 1
             ;;
     esac
@@ -633,6 +637,11 @@ update_all_existing_agents() {
         found_agent=true
     fi
     
+    if [[ -f "$ROO_FILE" ]]; then
+        update_agent_file "$ROO_FILE" "Roo Code"
+        found_agent=true
+    fi
+    
     # If no agent files exist, create a default Claude file
     if [[ "$found_agent" == false ]]; then
         log_info "No existing agent files found, creating default Claude file..."
@@ -656,7 +665,7 @@ print_summary() {
     fi
     
     echo
-    log_info "Usage: $0 [claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie]"
+    log_info "Usage: $0 [claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie|roo]"
 }
 
 #==============================================================================

scripts/powershell/check-prerequisites.ps1

@@ -63,14 +63,25 @@ if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit:$paths.HAS_GI
     exit 1 
 }
 
-# If paths-only mode, output paths and exit
+# If paths-only mode, output paths and exit (support combined -Json -PathsOnly)
 if ($PathsOnly) {
-    Write-Output "REPO_ROOT: $($paths.REPO_ROOT)"
-    Write-Output "BRANCH: $($paths.CURRENT_BRANCH)"
-    Write-Output "FEATURE_DIR: $($paths.FEATURE_DIR)"
-    Write-Output "FEATURE_SPEC: $($paths.FEATURE_SPEC)"
-    Write-Output "IMPL_PLAN: $($paths.IMPL_PLAN)"
-    Write-Output "TASKS: $($paths.TASKS)"
+    if ($Json) {
+        [PSCustomObject]@{
+            REPO_ROOT    = $paths.REPO_ROOT
+            BRANCH       = $paths.CURRENT_BRANCH
+            FEATURE_DIR  = $paths.FEATURE_DIR
+            FEATURE_SPEC = $paths.FEATURE_SPEC
+            IMPL_PLAN    = $paths.IMPL_PLAN
+            TASKS        = $paths.TASKS
+        } | ConvertTo-Json -Compress
+    } else {
+        Write-Output "REPO_ROOT: $($paths.REPO_ROOT)"
+        Write-Output "BRANCH: $($paths.CURRENT_BRANCH)"
+        Write-Output "FEATURE_DIR: $($paths.FEATURE_DIR)"
+        Write-Output "FEATURE_SPEC: $($paths.FEATURE_SPEC)"
+        Write-Output "IMPL_PLAN: $($paths.IMPL_PLAN)"
+        Write-Output "TASKS: $($paths.TASKS)"
+    }
     exit 0
 }
 

scripts/powershell/create-new-feature.ps1

@@ -89,7 +89,7 @@ if ($hasGit) {
 $featureDir = Join-Path $specsDir $branchName
 New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
 
-$template = Join-Path $repoRoot 'templates/spec-template.md'
+$template = Join-Path $repoRoot '.specify/templates/spec-template.md'
 $specFile = Join-Path $featureDir 'spec.md'
 if (Test-Path $template) { 
     Copy-Item $template $specFile -Force 

scripts/powershell/update-agent-context.ps1

@@ -25,7 +25,7 @@ Relies on common helper functions in common.ps1
 #>
 param(
     [Parameter(Position=0)]
-    [ValidateSet('claude','gemini','copilot','cursor','qwen','opencode','codex','windsurf','kilocode','auggie')]
+    [ValidateSet('claude','gemini','copilot','cursor','qwen','opencode','codex','windsurf','kilocode','auggie','roo')]
     [string]$AgentType
 )
 
@@ -53,6 +53,7 @@ $AGENTS_FILE   = Join-Path $REPO_ROOT 'AGENTS.md'
 $WINDSURF_FILE = Join-Path $REPO_ROOT '.windsurf/rules/specify-rules.md'
 $KILOCODE_FILE = Join-Path $REPO_ROOT '.kilocode/rules/specify-rules.md'
 $AUGGIE_FILE   = Join-Path $REPO_ROOT '.augment/rules/specify-rules.md'
+$ROO_FILE      = Join-Path $REPO_ROOT '.roo/rules/specify-rules.md'
 
 $TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'
 
@@ -374,7 +375,8 @@ function Update-SpecificAgent {
         'windsurf' { Update-AgentFile -TargetFile $WINDSURF_FILE -AgentName 'Windsurf' }
         'kilocode' { Update-AgentFile -TargetFile $KILOCODE_FILE -AgentName 'Kilo Code' }
         'auggie'   { Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI' }
-        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie'; return $false }
+        'roo'      { Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code' }
+        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie|roo'; return $false }
     }
 }
 
@@ -390,6 +392,7 @@ function Update-AllExistingAgents {
     if (Test-Path $WINDSURF_FILE) { if (-not (Update-AgentFile -TargetFile $WINDSURF_FILE -AgentName 'Windsurf')) { $ok = $false }; $found = $true }
     if (Test-Path $KILOCODE_FILE) { if (-not (Update-AgentFile -TargetFile $KILOCODE_FILE -AgentName 'Kilo Code')) { $ok = $false }; $found = $true }
     if (Test-Path $AUGGIE_FILE)   { if (-not (Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI')) { $ok = $false }; $found = $true }
+    if (Test-Path $ROO_FILE)      { if (-not (Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code')) { $ok = $false }; $found = $true }
     if (-not $found) {
         Write-Info 'No existing agent files found, creating default Claude file...'
         if (-not (Update-AgentFile -TargetFile $CLAUDE_FILE -AgentName 'Claude Code')) { $ok = $false }
@@ -404,7 +407,7 @@ function Print-Summary {
     if ($NEW_FRAMEWORK) { Write-Host "  - Added framework: $NEW_FRAMEWORK" }
     if ($NEW_DB -and $NEW_DB -ne 'N/A') { Write-Host "  - Added database: $NEW_DB" }
     Write-Host ''
-    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie]'
+    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor|qwen|opencode|codex|windsurf|kilocode|auggie|roo]'
 }
 
 function Main {

src/specify_cli/__init__.py

@@ -74,6 +74,7 @@ AI_CHOICES = {
     "windsurf": "Windsurf",
     "kilocode": "Kilo Code",
     "auggie": "Auggie CLI",
+    "roo": "Roo Code",
 }
 # Add script type choices
 SCRIPT_TYPE_CHOICES = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}
@@ -752,6 +753,7 @@ def init(
     ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for AI agent tools like Claude Code"),
     no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
     here: bool = typer.Option(False, "--here", help="Initialize project in the current directory instead of creating a new one"),
+    force: bool = typer.Option(False, "--force", help="Force merge/overwrite when using --here (skip confirmation)"),
     skip_tls: bool = typer.Option(False, "--skip-tls", help="Skip SSL/TLS verification (not recommended)"),
     debug: bool = typer.Option(False, "--debug", help="Show verbose diagnostic output for network and extraction failures"),
     github_token: str = typer.Option(None, "--github-token", help="GitHub token to use for API requests (or set GH_TOKEN or GITHUB_TOKEN environment variable)"),
@@ -782,6 +784,7 @@ def init(
         specify init --here --ai claude
         specify init --here --ai codex
         specify init --here
+        specify init --here --force  # Skip confirmation when current directory not empty
     """
     # Show banner first
     show_banner()
@@ -805,12 +808,14 @@ def init(
         if existing_items:
             console.print(f"[yellow]Warning:[/yellow] Current directory is not empty ({len(existing_items)} items)")
             console.print("[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]")
-            
-            # Ask for confirmation
-            response = typer.confirm("Do you want to continue?")
-            if not response:
-                console.print("[yellow]Operation cancelled[/yellow]")
-                raise typer.Exit(0)
+            if force:
+                console.print("[cyan]--force supplied: skipping confirmation and proceeding with merge[/cyan]")
+            else:
+                # Ask for confirmation
+                response = typer.confirm("Do you want to continue?")
+                if not response:
+                    console.print("[yellow]Operation cancelled[/yellow]")
+                    raise typer.Exit(0)
     else:
         project_path = Path(project_name).resolve()
         # Check if project directory already exists
@@ -1015,7 +1020,8 @@ def init(
         "windsurf": ".windsurf/",
         "kilocode": ".kilocode/",
         "auggie": ".augment/",
-        "copilot": ".github/"
+        "copilot": ".github/",
+        "roo": ".roo/"
     }
     
     if selected_ai in agent_folder_map:
@@ -1052,9 +1058,10 @@ def init(
         step_num += 1
 
     steps_lines.append(f"{step_num}. Start using slash commands with your AI agent:")
+
     steps_lines.append("   2.1 [cyan]/constitution[/] - Establish project principles")
-    steps_lines.append("   2.2 [cyan]/specify[/] - Create specifications")
-    steps_lines.append("   2.3 [cyan]/plan[/] - Create implementation plans")
+    steps_lines.append("   2.2 [cyan]/specify[/] - Create baseline specification")
+    steps_lines.append("   2.3 [cyan]/plan[/] - Create implementation plan")
     steps_lines.append("   2.4 [cyan]/tasks[/] - Generate actionable tasks")
     steps_lines.append("   2.5 [cyan]/implement[/] - Execute implementation")
 
@@ -1062,6 +1069,16 @@ def init(
     console.print()
     console.print(steps_panel)
 
+    enhancement_lines = [
+        "Optional commands that you can use for your specs (improve quality & confidence)[/bright_black]",
+        "",
+        f"○ [cyan]/clarify[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]/plan[/] if used)",
+        f"○ [cyan]/analyze[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]/tasks[/], before [cyan]/implement[/])"
+    ]
+    enhancements_panel = Panel("\n".join(enhancement_lines), title="Enhancement Commands", border_style="cyan", padding=(1,2))
+    console.print()
+    console.print(enhancements_panel)
+
     if selected_ai == "codex":
         warning_text = """[bold yellow]Important Note:[/bold yellow]
 

templates/commands/analyze.md

@@ -0,0 +1,104 @@
+---
+description: Perform a non-destructive cross-artifact consistency and quality analysis across spec.md, plan.md, and tasks.md after task generation.
+scripts:
+  sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
+  ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+---
+
+The user input to you can be provided directly by the agent or as a command argument - you **MUST** consider it before proceeding with the prompt (if not empty).
+
+User input:
+
+$ARGUMENTS
+
+Goal: Identify inconsistencies, duplications, ambiguities, and underspecified items across the three core artifacts (`spec.md`, `plan.md`, `tasks.md`) before implementation. This command MUST run only after `/tasks` has successfully produced a complete `tasks.md`.
+
+STRICTLY READ-ONLY: Do **not** modify any files. Output a structured analysis report. Offer an optional remediation plan (user must explicitly approve before any follow-up editing commands would be invoked manually).
+
+Constitution Authority: The project constitution (`/memory/constitution.md`) is **non-negotiable** within this analysis scope. Constitution conflicts are automatically CRITICAL and require adjustment of the spec, plan, or tasks—not dilution, reinterpretation, or silent ignoring of the principle. If a principle itself needs to change, that must occur in a separate, explicit constitution update outside `/analyze`.
+
+Execution steps:
+
+1. Run `{SCRIPT}` once from repo root and parse JSON for FEATURE_DIR and AVAILABLE_DOCS. Derive absolute paths:
+   - SPEC = FEATURE_DIR/spec.md
+   - PLAN = FEATURE_DIR/plan.md
+   - TASKS = FEATURE_DIR/tasks.md
+   Abort with an error message if any required file is missing (instruct the user to run missing prerequisite command).
+
+2. Load artifacts:
+   - Parse spec.md sections: Overview/Context, Functional Requirements, Non-Functional Requirements, User Stories, Edge Cases (if present).
+   - Parse plan.md: Architecture/stack choices, Data Model references, Phases, Technical constraints.
+   - Parse tasks.md: Task IDs, descriptions, phase grouping, parallel markers [P], referenced file paths.
+   - Load constitution `/memory/constitution.md` for principle validation.
+
+3. Build internal semantic models:
+   - Requirements inventory: Each functional + non-functional requirement with a stable key (derive slug based on imperative phrase; e.g., "User can upload file" -> `user-can-upload-file`).
+   - User story/action inventory.
+   - Task coverage mapping: Map each task to one or more requirements or stories (inference by keyword / explicit reference patterns like IDs or key phrases).
+   - Constitution rule set: Extract principle names and any MUST/SHOULD normative statements.
+
+4. Detection passes:
+   A. Duplication detection:
+      - Identify near-duplicate requirements. Mark lower-quality phrasing for consolidation.
+   B. Ambiguity detection:
+      - Flag vague adjectives (fast, scalable, secure, intuitive, robust) lacking measurable criteria.
+      - Flag unresolved placeholders (TODO, TKTK, ???, <placeholder>, etc.).
+   C. Underspecification:
+      - Requirements with verbs but missing object or measurable outcome.
+      - User stories missing acceptance criteria alignment.
+      - Tasks referencing files or components not defined in spec/plan.
+   D. Constitution alignment:
+      - Any requirement or plan element conflicting with a MUST principle.
+      - Missing mandated sections or quality gates from constitution.
+   E. Coverage gaps:
+      - Requirements with zero associated tasks.
+      - Tasks with no mapped requirement/story.
+      - Non-functional requirements not reflected in tasks (e.g., performance, security).
+   F. Inconsistency:
+      - Terminology drift (same concept named differently across files).
+      - Data entities referenced in plan but absent in spec (or vice versa).
+      - Task ordering contradictions (e.g., integration tasks before foundational setup tasks without dependency note).
+      - Conflicting requirements (e.g., one requires to use Next.js while other says to use Vue as the framework).
+
+5. Severity assignment heuristic:
+   - CRITICAL: Violates constitution MUST, missing core spec artifact, or requirement with zero coverage that blocks baseline functionality.
+   - HIGH: Duplicate or conflicting requirement, ambiguous security/performance attribute, untestable acceptance criterion.
+   - MEDIUM: Terminology drift, missing non-functional task coverage, underspecified edge case.
+   - LOW: Style/wording improvements, minor redundancy not affecting execution order.
+
+6. Produce a Markdown report (no file writes) with sections:
+
+   ### Specification Analysis Report
+   | ID | Category | Severity | Location(s) | Summary | Recommendation |
+   |----|----------|----------|-------------|---------|----------------|
+   | A1 | Duplication | HIGH | spec.md:L120-134 | Two similar requirements ... | Merge phrasing; keep clearer version |
+   (Add one row per finding; generate stable IDs prefixed by category initial.)
+
+   Additional subsections:
+   - Coverage Summary Table:
+     | Requirement Key | Has Task? | Task IDs | Notes |
+   - Constitution Alignment Issues (if any)
+   - Unmapped Tasks (if any)
+   - Metrics:
+     * Total Requirements
+     * Total Tasks
+     * Coverage % (requirements with >=1 task)
+     * Ambiguity Count
+     * Duplication Count
+     * Critical Issues Count
+
+7. At end of report, output a concise Next Actions block:
+   - If CRITICAL issues exist: Recommend resolving before `/implement`.
+   - If only LOW/MEDIUM: User may proceed, but provide improvement suggestions.
+   - Provide explicit command suggestions: e.g., "Run /specify with refinement", "Run /plan to adjust architecture", "Manually edit tasks.md to add coverage for 'performance-metrics'".
+
+8. Ask the user: "Would you like me to suggest concrete remediation edits for the top N issues?" (Do NOT apply them automatically.)
+
+Behavior rules:
+- NEVER modify files.
+- NEVER hallucinate missing sections—if absent, report them.
+- KEEP findings deterministic: if rerun without changes, produce consistent IDs and counts.
+- LIMIT total findings in the main table to 50; aggregate remainder in a summarized overflow note.
+- If zero issues found, emit a success report with coverage statistics and proceed recommendation.
+
+Context: {ARGS}

templates/commands/clarify.md

@@ -0,0 +1,161 @@
+---
+description: Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
+scripts:
+   sh: scripts/bash/check-prerequisites.sh --json --paths-only
+   ps: scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly
+---
+
+The user input to you can be provided directly by the agent or as a command argument - you **MUST** consider it before proceeding with the prompt (if not empty).
+
+User input:
+
+$ARGUMENTS
+
+Goal: Detect and reduce ambiguity or missing decision points in the active feature specification and record the clarifications directly in the spec file.
+
+Note: This clarification workflow is expected to run (and be completed) BEFORE invoking `/plan`. If the user explicitly states they are skipping clarification (e.g., exploratory spike), you may proceed, but must warn that downstream rework risk increases.
+
+Execution steps:
+
+1. Run `{SCRIPT}` from repo root **once** (combined `--json --paths-only` mode / `-Json -PathsOnly`). Parse minimal JSON payload fields:
+   - `FEATURE_DIR`
+   - `FEATURE_SPEC`
+   - (Optionally capture `IMPL_PLAN`, `TASKS` for future chained flows.)
+   - If JSON parsing fails, abort and instruct user to re-run `/specify` or verify feature branch environment.
+
+2. Load the current spec file. Perform a structured ambiguity & coverage scan using this taxonomy. For each category, mark status: Clear / Partial / Missing. Produce an internal coverage map used for prioritization (do not output raw map unless no questions will be asked).
+
+   Functional Scope & Behavior:
+   - Core user goals & success criteria
+   - Explicit out-of-scope declarations
+   - User roles / personas differentiation
+
+   Domain & Data Model:
+   - Entities, attributes, relationships
+   - Identity & uniqueness rules
+   - Lifecycle/state transitions
+   - Data volume / scale assumptions
+
+   Interaction & UX Flow:
+   - Critical user journeys / sequences
+   - Error/empty/loading states
+   - Accessibility or localization notes
+
+   Non-Functional Quality Attributes:
+   - Performance (latency, throughput targets)
+   - Scalability (horizontal/vertical, limits)
+   - Reliability & availability (uptime, recovery expectations)
+   - Observability (logging, metrics, tracing signals)
+   - Security & privacy (authN/Z, data protection, threat assumptions)
+   - Compliance / regulatory constraints (if any)
+
+   Integration & External Dependencies:
+   - External services/APIs and failure modes
+   - Data import/export formats
+   - Protocol/versioning assumptions
+
+   Edge Cases & Failure Handling:
+   - Negative scenarios
+   - Rate limiting / throttling
+   - Conflict resolution (e.g., concurrent edits)
+
+   Constraints & Tradeoffs:
+   - Technical constraints (language, storage, hosting)
+   - Explicit tradeoffs or rejected alternatives
+
+   Terminology & Consistency:
+   - Canonical glossary terms
+   - Avoided synonyms / deprecated terms
+
+   Completion Signals:
+   - Acceptance criteria testability
+   - Measurable Definition of Done style indicators
+
+   Misc / Placeholders:
+   - TODO markers / unresolved decisions
+   - Ambiguous adjectives ("robust", "intuitive") lacking quantification
+
+   For each category with Partial or Missing status, add a candidate question opportunity unless:
+   - Clarification would not materially change implementation or validation strategy
+   - Information is better deferred to planning phase (note internally)
+
+3. Generate (internally) a prioritized queue of candidate clarification questions (maximum 5). Do NOT output them all at once. Apply these constraints:
+    - Maximum of 5 total questions across the whole session.
+    - Each question must be answerable with EITHER:
+       * A short multiple‑choice selection (2–5 distinct, mutually exclusive options), OR
+       * A one-word / short‑phrase answer (explicitly constrain: "Answer in <=5 words").
+   - Only include questions whose answers materially impact architecture, data modeling, task decomposition, test design, UX behavior, operational readiness, or compliance validation.
+   - Ensure category coverage balance: attempt to cover the highest impact unresolved categories first; avoid asking two low-impact questions when a single high-impact area (e.g., security posture) is unresolved.
+   - Exclude questions already answered, trivial stylistic preferences, or plan-level execution details (unless blocking correctness).
+   - Favor clarifications that reduce downstream rework risk or prevent misaligned acceptance tests.
+   - If more than 5 categories remain unresolved, select the top 5 by (Impact * Uncertainty) heuristic.
+
+4. Sequential questioning loop (interactive):
+    - Present EXACTLY ONE question at a time.
+    - For multiple‑choice questions render options as a Markdown table:
+
+       | Option | Description |
+       |--------|-------------|
+       | A | <Option A description> |
+       | B | <Option B description> |
+       | C | <Option C description> | (add D/E as needed up to 5)
+       | Short | Provide a different short answer (<=5 words) | (Include only if free-form alternative is appropriate)
+
+    - For short‑answer style (no meaningful discrete options), output a single line after the question: `Format: Short answer (<=5 words)`.
+    - After the user answers:
+       * Validate the answer maps to one option or fits the <=5 word constraint.
+       * If ambiguous, ask for a quick disambiguation (count still belongs to same question; do not advance).
+       * Once satisfactory, record it in working memory (do not yet write to disk) and move to the next queued question.
+    - Stop asking further questions when:
+       * All critical ambiguities resolved early (remaining queued items become unnecessary), OR
+       * User signals completion ("done", "good", "no more"), OR
+       * You reach 5 asked questions.
+    - Never reveal future queued questions in advance.
+    - If no valid questions exist at start, immediately report no critical ambiguities.
+
+5. Integration after EACH accepted answer (incremental update approach):
+    - Maintain in-memory representation of the spec (loaded once at start) plus the raw file contents.
+    - For the first integrated answer in this session:
+       * Ensure a `## Clarifications` section exists (create it just after the highest-level contextual/overview section per the spec template if missing).
+       * Under it, create (if not present) a `### Session YYYY-MM-DD` subheading for today.
+    - Append a bullet line immediately after acceptance: `- Q: <question> → A: <final answer>`.
+    - Then immediately apply the clarification to the most appropriate section(s):
+       * Functional ambiguity → Update or add a bullet in Functional Requirements.
+       * User interaction / actor distinction → Update User Stories or Actors subsection (if present) with clarified role, constraint, or scenario.
+       * Data shape / entities → Update Data Model (add fields, types, relationships) preserving ordering; note added constraints succinctly.
+       * Non-functional constraint → Add/modify measurable criteria in Non-Functional / Quality Attributes section (convert vague adjective to metric or explicit target).
+       * Edge case / negative flow → Add a new bullet under Edge Cases / Error Handling (or create such subsection if template provides placeholder for it).
+       * Terminology conflict → Normalize term across spec; retain original only if necessary by adding `(formerly referred to as "X")` once.
+    - If the clarification invalidates an earlier ambiguous statement, replace that statement instead of duplicating; leave no obsolete contradictory text.
+    - Save the spec file AFTER each integration to minimize risk of context loss (atomic overwrite).
+    - Preserve formatting: do not reorder unrelated sections; keep heading hierarchy intact.
+    - Keep each inserted clarification minimal and testable (avoid narrative drift).
+
+6. Validation (performed after EACH write plus final pass):
+   - Clarifications session contains exactly one bullet per accepted answer (no duplicates).
+   - Total asked (accepted) questions ≤ 5.
+   - Updated sections contain no lingering vague placeholders the new answer was meant to resolve.
+   - No contradictory earlier statement remains (scan for now-invalid alternative choices removed).
+   - Markdown structure valid; only allowed new headings: `## Clarifications`, `### Session YYYY-MM-DD`.
+   - Terminology consistency: same canonical term used across all updated sections.
+
+7. Write the updated spec back to `FEATURE_SPEC`.
+
+8. Report completion (after questioning loop ends or early termination):
+   - Number of questions asked & answered.
+   - Path to updated spec.
+   - Sections touched (list names).
+   - Coverage summary table listing each taxonomy category with Status: Resolved (was Partial/Missing and addressed), Deferred (exceeds question quota or better suited for planning), Clear (already sufficient), Outstanding (still Partial/Missing but low impact).
+   - If any Outstanding or Deferred remain, recommend whether to proceed to `/plan` or run `/clarify` again later post-plan.
+   - Suggested next command.
+
+Behavior rules:
+- If no meaningful ambiguities found (or all potential questions would be low-impact), respond: "No critical ambiguities detected worth formal clarification." and suggest proceeding.
+- If spec file missing, instruct user to run `/specify` first (do not create a new spec here).
+- Never exceed 5 total asked questions (clarification retries for a single question do not count as new questions).
+- Avoid speculative tech stack questions unless the absence blocks functional clarity.
+- Respect user early termination signals ("stop", "done", "proceed").
+ - If no questions asked due to full coverage, output a compact coverage summary (all categories Clear) then suggest advancing.
+ - If quota reached with unresolved high-impact categories remaining, explicitly flag them under Deferred with rationale.
+
+Context for prioritization: {ARGS}

templates/commands/plan.md

@@ -14,6 +14,7 @@ $ARGUMENTS
 Given the implementation details provided as an argument, do this:
 
 1. Run `{SCRIPT}` from the repo root and parse JSON for FEATURE_SPEC, IMPL_PLAN, SPECS_DIR, BRANCH. All future file paths must be absolute.
+   - BEFORE proceeding, inspect FEATURE_SPEC for a `## Clarifications` section with at least one `Session` subheading. If missing or clearly ambiguous areas remain (vague adjectives, unresolved critical choices), PAUSE and instruct the user to run `/clarify` first to reduce rework. Only continue if: (a) Clarifications exist OR (b) an explicit user override is provided (e.g., "proceed without clarification"). Do not attempt to fabricate clarifications yourself.
 2. Read and analyze the feature specification to understand:
    - The feature requirements and user stories
    - Functional and non-functional requirements

templates/plan-template.md

@@ -15,7 +15,7 @@ scripts:
 1. Load feature spec from Input path
    → If not found: ERROR "No feature spec at {path}"
 2. Fill Technical Context (scan for NEEDS CLARIFICATION)
-   → Detect Project Type from context (web=frontend+backend, mobile=app+api)
+   → Detect Project Type from file system structure or context (web=frontend+backend, mobile=app+api)
    → Set Structure Decision based on project type
 3. Fill the Constitution Check section based on the content of the constitution document.
 4. Evaluate Constitution Check section below
@@ -69,8 +69,14 @@ specs/[###-feature]/
 ```
 
 ### Source Code (repository root)
+<!--
+  ACTION REQUIRED: Replace the placeholder tree below with the concrete layout
+  for this feature. Delete unused options and expand the chosen structure with
+  real paths (e.g., apps/admin, packages/something). The delivered plan must
+  not include Option labels.
+-->
 ```
-# Option 1: Single project (DEFAULT)
+# [REMOVE IF UNUSED] Option 1: Single project (DEFAULT)
 src/
 ├── models/
 ├── services/
@@ -82,7 +88,7 @@ tests/
 ├── integration/
 └── unit/
 
-# Option 2: Web application (when "frontend" + "backend" detected)
+# [REMOVE IF UNUSED] Option 2: Web application (when "frontend" + "backend" detected)
 backend/
 ├── src/
 │   ├── models/
@@ -97,15 +103,16 @@ frontend/
 │   └── services/
 └── tests/
 
-# Option 3: Mobile + API (when "iOS/Android" detected)
+# [REMOVE IF UNUSED] Option 3: Mobile + API (when "iOS/Android" detected)
 api/
 └── [same as backend above]
 
 ios/ or android/
-└── [platform-specific structure]
+└── [platform-specific structure: feature modules, UI flows, platform tests]
 ```
 
-**Structure Decision**: [DEFAULT to Option 1 unless Technical Context indicates web/mobile app]
+**Structure Decision**: [Document the selected structure and reference the real
+directories captured above]
 
 ## Phase 0: Outline & Research
 1. **Extract unknowns from Technical Context** above: