feat: deliver TOC navigation as a preset (closes #1970)

Pivots from core template changes to a preset approach per reviewer
request. Adds presets/toc-navigation/ with 3 template overrides and
3 command overrides that add Table of Contents sections to generated
spec.md, plan.md, and tasks.md documents.

Addresses all 8 impact concerns from review:
- Templates use anchor links (not plain text) matching command instructions
- All 12 tasks-template headings accounted for (dynamic phases as plain text)
- spec-template anchors include -mandatory suffix
- TOC placed after Note paragraph in plan-template
- Self-reference exclusion explicit in all commands
- Clarify stale TOC instruction in specify command
- Implement misparse warning in tasks command

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Quratulain-bilal

presets/toc-navigation/commands/speckit.plan.md

@@ -0,0 +1,160 @@
+---
+description: Execute the implementation planning workflow using the plan template to generate design artifacts.
+handoffs: 
+  - label: Create Tasks
+    agent: speckit.tasks
+    prompt: Break the plan into tasks
+    send: true
+  - label: Create Checklist
+    agent: speckit.checklist
+    prompt: Create a checklist for the following domain...
+scripts:
+  sh: scripts/bash/setup-plan.sh --json
+  ps: scripts/powershell/setup-plan.ps1 -Json
+agent_scripts:
+  sh: scripts/bash/update-agent-context.sh __AGENT__
+  ps: scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
+---
+
+## User Input
+
+```text
+$ARGUMENTS
+```
+
+You **MUST** consider the user input before proceeding (if not empty).
+
+## Pre-Execution Checks
+
+**Check for extension hooks (before planning)**:
+- Check if `.specify/extensions.yml` exists in the project root.
+- If it exists, read it and look for entries under the `hooks.before_plan` key
+- If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
+- Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+- For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
+  - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
+  - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
+- For each executable hook, output the following based on its `optional` flag:
+  - **Optional hook** (`optional: true`):
+    ```
+    ## Extension Hooks
+
+    **Optional Pre-Hook**: {extension}
+    Command: `/{command}`
+    Description: {description}
+
+    Prompt: {prompt}
+    To execute: `/{command}`
+    ```
+  - **Mandatory hook** (`optional: false`):
+    ```
+    ## Extension Hooks
+
+    **Automatic Pre-Hook**: {extension}
+    Executing: `/{command}`
+    EXECUTE_COMMAND: {command}
+
+    Wait for the result of the hook command before proceeding to the Outline.
+    ```
+- If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
+
+## Outline
+
+1. **Setup**: Run `{SCRIPT}` from repo root and parse JSON for FEATURE_SPEC, IMPL_PLAN, SPECS_DIR, BRANCH. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
+
+2. **Load context**: Read FEATURE_SPEC and `/memory/constitution.md`. Load IMPL_PLAN template (already copied).
+
+3. **Execute plan workflow**: Follow the structure in IMPL_PLAN template to:
+   - Include a `## Table of Contents` section immediately after the title and initial metadata lines (Branch, Date, Spec, Input, Note) and before the `## Summary` section. List every `##`-level heading in the final document as a markdown anchor link using GitHub-style anchors (lowercase, spaces to hyphens, strip special characters). Do **not** include a self-referencing entry for `## Table of Contents` itself. Only include headings that actually appear in the final document.
+   - Fill Technical Context (mark unknowns as "NEEDS CLARIFICATION")
+   - Fill Constitution Check section from constitution
+   - Evaluate gates (ERROR if violations unjustified)
+   - Phase 0: Generate research.md (resolve all NEEDS CLARIFICATION)
+   - Phase 1: Generate data-model.md, contracts/, quickstart.md
+   - Phase 1: Update agent context by running the agent script
+   - Re-evaluate Constitution Check post-design
+
+4. **Stop and report**: Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.
+
+5. **Check for extension hooks**: After reporting, check if `.specify/extensions.yml` exists in the project root.
+   - If it exists, read it and look for entries under the `hooks.after_plan` key
+   - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
+   - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.
+   - For each remaining hook, do **not** attempt to interpret or evaluate hook `condition` expressions:
+     - If the hook has no `condition` field, or it is null/empty, treat the hook as executable
+     - If the hook defines a non-empty `condition`, skip the hook and leave condition evaluation to the HookExecutor implementation
+   - For each executable hook, output the following based on its `optional` flag:
+     - **Optional hook** (`optional: true`):
+       ```
+       ## Extension Hooks
+
+       **Optional Hook**: {extension}
+       Command: `/{command}`
+       Description: {description}
+
+       Prompt: {prompt}
+       To execute: `/{command}`
+       ```
+     - **Mandatory hook** (`optional: false`):
+       ```
+       ## Extension Hooks
+
+       **Automatic Hook**: {extension}
+       Executing: `/{command}`
+       EXECUTE_COMMAND: {command}
+       ```
+   - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
+
+## Phases
+
+### Phase 0: Outline & Research
+
+1. **Extract unknowns from Technical Context** above:
+   - For each NEEDS CLARIFICATION → research task
+   - For each dependency → best practices task
+   - For each integration → patterns task
+
+2. **Generate and dispatch research agents**:
+
+   ```text
+   For each unknown in Technical Context:
+     Task: "Research {unknown} for {feature context}"
+   For each technology choice:
+     Task: "Find best practices for {tech} in {domain}"
+   ```
+
+3. **Consolidate findings** in `research.md` using format:
+   - Decision: [what was chosen]
+   - Rationale: [why chosen]
+   - Alternatives considered: [what else evaluated]
+
+**Output**: research.md with all NEEDS CLARIFICATION resolved
+
+### Phase 1: Design & Contracts
+
+**Prerequisites:** `research.md` complete
+
+1. **Extract entities from feature spec** → `data-model.md`:
+   - Entity name, fields, relationships
+   - Validation rules from requirements
+   - State transitions if applicable
+
+2. **Define interface contracts** (if project has external interfaces) → `/contracts/`:
+   - Identify what interfaces the project exposes to users or other systems
+   - Document the contract format appropriate for the project type
+   - Examples: public APIs for libraries, command schemas for CLI tools, endpoints for web services, grammars for parsers, UI contracts for applications
+   - Skip if project is purely internal (build scripts, one-off tools, etc.)
+
+3. **Agent context update**:
+   - Run `{AGENT_SCRIPT}`
+   - These scripts detect which AI agent is in use
+   - Update the appropriate agent-specific context file
+   - Add only new technology from current plan
+   - Preserve manual additions between markers
+
+**Output**: data-model.md, /contracts/*, quickstart.md, agent-specific file
+
+## Key rules
+
+- Use absolute paths
+- ERROR on gate failures or unresolved clarifications