Fix constitution-preset-template-sync: discover and propagate to all effective template layers

Apply the remediation from the bug assessment on issue #3737.
Update the constitution command template (step 4) to resolve the full
effective template stack for plan-template, spec-template, and
tasks-template before propagating constitutional guidance. The agent now
discovers project-local overrides and all active preset-provided
replacements (via .specify/presets/*/preset.yml replaces fields) and
propagates to every layer, not just the hard-coded built-in path.
Step 5 (Sync Impact Report) is updated to derive entries from the
resolved stack and only mark templates as updated when actually reviewed.

Refs #3737

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Author: github-actions[bot]

templates/commands/constitution.md

@@ -97,9 +97,33 @@ Follow this execution flow:
    - Ensure Governance section lists amendment procedure, versioning policy, and compliance review expectations.
 
 4. Consistency propagation checklist (convert prior checklist into active validations):
-   - Read `.specify/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
-   - Read `.specify/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
-   - Read `.specify/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
+
+   **Before reading any template, resolve the full effective template stack for each governed template type.**
+   For each of the three governed templates — `plan-template`, `spec-template`, and `tasks-template` — perform this discovery:
+
+   a. **Discover all active layers** (in priority order):
+      1. **Project-local override**: Check if `.specify/templates/<template-name>.md` exists. If so, include it.
+      2. **Active preset-provided replacements**: List every subdirectory of `.specify/presets/` (if the directory exists).
+         For each subdirectory, read `preset.yml` and look for entries under `provides.templates` where the `replaces`
+         field matches `<template-name>`. For each matching entry, the preset-provided file path is
+         `.specify/presets/<preset-id>/<file>` (the `file` field from `preset.yml`). Include all such files.
+      3. **Core/built-in reference**: Note that the core template in the package itself is not directly editable
+         by the agent; treat it as the canonical reference for constitutional guidance.
+
+   b. **Propagate constitutional guidance to every discovered layer** (project-local overrides and preset-provided
+      replacements). For each discovered file:
+      - Read the file.
+      - Ensure any "Constitution Check" sections, rules, task categories, or scope/requirements constraints align
+        with the updated principles.
+      - Preserve the file's existing structure, specialized content, and provider-specific generation behavior —
+        do **not** overwrite provider-specific sections with generic content from a different layer.
+      - Write back only if changes are needed; otherwise mark as already-compliant.
+
+   c. **Fallback (no active layers found)**: If no project-local override or preset-provided replacement exists for
+      a template, note in the Sync Impact Report that no installed copy was found and the core template (read-only)
+      is the effective source.
+
+   After resolving all three template types, also:
    - Read each installed Spec Kit command file for your agent (including this one) — named `speckit.*` or `speckit-*` (dot or hyphen depending on the agent), or laid out as `speckit-<name>/SKILL.md` for skills-based integrations, e.g. in `.github/agents/`, `.github/skills/`, `.claude/skills/`, or your agent's equivalent commands directory — to verify no outdated references (CLAUDE-only or other agent-specific names) remain when generic guidance is required.
    - Read any runtime guidance docs (e.g., `README.md`, `docs/quickstart.md`, or agent-specific guidance files if present). Update references to principles changed.
 
@@ -108,7 +132,11 @@ Follow this execution flow:
    - List of modified principles (old title → new title if renamed)
    - Added sections
    - Removed sections
-   - Templates requiring updates (✅ updated / ⚠ pending) with file paths
+   - Templates requiring updates (✅ updated / ⚠ pending / ✗ not found) — list **every** resolved template layer
+     from step 4 (project-local overrides and preset-provided replacements) with its file path and provider
+     (e.g., "project override", "preset: <preset-id>"). A template must only be marked ✅ updated if it was
+     actually reviewed and either modified or explicitly verified as already compliant during this run. Templates
+     that were not reviewed in this run must be marked ⚠ pending.
    - Follow-up TODOs if any placeholders intentionally deferred.
 
 6. Validation before final output: