docs: deprecate .specify specs and update references

.specify/README.md

@@ -0,0 +1,14 @@
+# `.specify/` (Tooling)
+
+This folder contains **SpecKit tooling** (templates, scripts, constitution, etc.).
+
+## Important
+
+- **Do not** create new feature specs in `.specify/spec.md`, `.specify/plan.md`, `.specify/tasks.md`.
+- Active feature specs live under `specs/<NNN>-<slug>/`:
+  - `spec.md`
+  - `plan.md`
+  - `tasks.md`
+  - `checklists/requirements.md`
+
+The files `.specify/spec.md`, `.specify/plan.md`, `.specify/tasks.md` may exist as legacy references only.

.specify/plan.md

@@ -1,4 +1,8 @@
-# Implementation Plan: TenantPilot v1
+# Implementation Plan: TenantPilot v1 (LEGACY / DEPRECATED)
+
+> DEPRECATED: Do not use `.specify/plan.md` for new work.
+> Active feature plans live under `specs/<NNN>-<slug>/plan.md` on `feat/<NNN>-<slug>` branches.
+> Legacy history lives under `spechistory/`.
 
 **Branch**: `dev`  
 **Date**: 2026-01-03  

.specify/research_t186.md

@@ -1,4 +1,8 @@
-# Research T186 — settings_apply capability verification
+# Research T186 — settings_apply capability verification (LEGACY / DEPRECATED)
+
+> DEPRECATED: Do not add new research notes under `.specify/`.
+> Active feature research should live under `specs/<NNN>-<slug>/`.
+> Legacy history lives under `spechistory/`.
 
 Objective
 ---------

.specify/spec.md

@@ -1,4 +1,8 @@
-# Feature Specification: TenantPilot v1
+# Feature Specification: TenantPilot v1 (LEGACY / DEPRECATED)
+
+> DEPRECATED: Do not use `.specify/spec.md` for new work.
+> Active feature specs live under `specs/<NNN>-<slug>/spec.md` on `feat/<NNN>-<slug>` branches.
+> Legacy history lives under `spechistory/`.
 
 **Feature Branch**: `dev`  
 **Created**: 2025-12-10  

.specify/tasks.md

@@ -2,7 +2,11 @@
 description: "Task list for TenantPilot v1 implementation"
 ---
 
-# Tasks: TenantPilot v1
+# Tasks: TenantPilot v1 (LEGACY / DEPRECATED)
+
+> DEPRECATED: Do not use `.specify/tasks.md` for new work.
+> Active feature task lists live under `specs/<NNN>-<slug>/tasks.md` on `feat/<NNN>-<slug>` branches.
+> Legacy history lives under `spechistory/`.
 
 **Input**: Design documents from `.specify/spec.md` and `.specify/plan.md`  
 **Prerequisites**: plan.md (complete), spec.md (complete)

Agents.md

@@ -26,9 +26,9 @@ ## Scope Reference
 
 ## Workflow (Spec Kit)
 1. Read `.specify/constitution.md`
-2. For new work: create/update `.specify/spec.md`
+2. For new work: create/update `specs/<NNN>-<slug>/spec.md`
-3. Produce `.specify/plan.md`
+3. Produce `specs/<NNN>-<slug>/plan.md`
-4. Break into `.specify/tasks.md`
+4. Break into `specs/<NNN>-<slug>/tasks.md`
 5. Implement changes in small PRs
 
 If requirements change during implementation, update spec/plan before continuing.
@@ -270,7 +270,7 @@ ## Engineering Rules
 - Keep Microsoft Graph integration isolated behind a dedicated abstraction layer.
 - Use dependency injection and clear interfaces for Graph clients.
 - No breaking changes to data structures or API contracts without updating:
-  - `.specify/spec.md`
+  - `specs/<NNN>-<slug>/spec.md`
   - migration notes
   - upgrade steps
 - If a TypeScript/JS tooling package exists, use strict typing rules there too.

GEMINI.md

@@ -26,9 +26,9 @@ ## Scope Reference
 
 ## Workflow (Spec Kit)
 1. Read `.specify/constitution.md`
-2. For new work: create/update `.specify/spec.md`
+2. For new work: create/update `specs/<NNN>-<slug>/spec.md`
-3. Produce `.specify/plan.md`
+3. Produce `specs/<NNN>-<slug>/plan.md`
-4. Break into `.specify/tasks.md`
+4. Break into `specs/<NNN>-<slug>/tasks.md`
 5. Implement changes in small PRs
 
 If requirements change during implementation, update spec/plan before continuing.
@@ -110,7 +110,7 @@ ## Engineering Rules
 - Keep Microsoft Graph integration isolated behind a dedicated abstraction layer.
 - Use dependency injection and clear interfaces for Graph clients.
 - No breaking changes to data structures or API contracts without updating:
-  - `.specify/spec.md`
+  - `specs/<NNN>-<slug>/spec.md`
   - migration notes
   - upgrade steps
 - If a TypeScript/JS tooling package exists, use strict typing rules there too.

specs/001-rbac-onboarding/tasks.md

@@ -4,7 +4,7 @@
 
 # Tasks: TenantPilot v1
 
-**Input**: Design documents from `.specify/spec.md` and `.specify/plan.md`
+**Input**: `specs/001-rbac-onboarding/spec.md` and `specs/001-rbac-onboarding/plan.md`  
 **Prerequisites**: plan.md (complete), spec.md (complete)
 
 ---

specs/004-assignments-scope-tags/plan.md

@@ -323,7 +323,7 @@ ### Phase 10: Deployment & Documentation
    - Run migrations on staging
    - Verify no data loss
    - Test on production-like data volume
-2. Update `.specify/spec.md` with implementation notes
+2. Update `specs/004-assignments-scope-tags/spec.md` with implementation notes
 3. Create migration guide for existing backups (no retroactive assignment capture)
 4. Add monitoring alerts:
    - Assignment fetch failure rate > 10%

specs/008-apps-app-management/spec.md

@@ -3,7 +3,7 @@ # Feature Specification: Apps (Mobile Apps) Metadata-Only + Assignments
 **Feature Branch**: `feat/008-apps-app-management`  
 **Created**: 2025-12-29  
 **Status**: Draft  
-**Input**: `.specify/spec.md` (mobileApp scope) + `references/IntuneManagement-master/Documentation/AppTypes.json` (known app @odata.type values).
+**Input**: `spechistory/spec.md` (legacy v1 scope) + `references/IntuneManagement-master/Documentation/AppTypes.json` (known app @odata.type values).
 
 ## Overview
 Add reliable **mobile app** (`mobileApp`) coverage for inventory, backup/version capture, and restore:

specs/010-admin-templates/spec.md

@@ -3,7 +3,7 @@ # Feature Specification: Administrative Templates (Group Policy Configurations)
 **Feature Branch**: `feat/010-admin-templates`  
 **Created**: 2025-12-29  
 **Status**: Draft  
-**Input**: `.specify/spec.md` (groupPolicyConfiguration scope), `references/IntuneManagement-master` (definitionValues/presentationValues pattern)
+**Input**: `spechistory/spec.md` (legacy v1 scope), `references/IntuneManagement-master` (definitionValues/presentationValues pattern)
 
 ## Overview
 Add reliable coverage for **Administrative Templates** (`groupPolicyConfiguration`) in the existing inventory/backup/version/restore flows.