refactor!: remove all materialize and migrate traces

Remove the last remnants of the long-deprecated `materialize` command and
delete the deprecated `migrate` command outright.

materialize (already removed as a command):
- Rename internal `materialized`/`materialized_files` identifiers to
  `template_files` across the git engine and sync command.
- Reword docstrings, log messages, and tests (materialize -> sync/copy/write).
- Drop leftover doc sections, Makefile target, and CHANGELOG mentions.

migrate (BREAKING — public command removed):
- Delete `commands/migrate.py` and its test suite.
- Remove the CLI registration and command.
- Replace the `rhiza migrate` recovery hint in `validate` with manual
  move guidance.
- Remove doc sections and scrub incidental "migrate/migration" wording.

Gates: 649 tests pass, ruff check/format clean, mypy clean, interrogate 100%.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: tschm

.pre-commit-config.yaml

@@ -90,7 +90,7 @@ repos:
   - repo: https://github.com/Jebel-Quant/rhiza-hooks
     rev: v0.7.0  # Use the latest release
     hooks:
-      # Migrated from rhiza
+      # Adopted from rhiza
       - id: check-rhiza-workflow-names
       - id: update-readme-help
       # Additional utility hooks

.rhiza/rhiza.mk

@@ -135,7 +135,7 @@ endef
 export RHIZA_LOGO
 
 # Declare phony targets for Rhiza Core
-.PHONY: print-logo sync sync-experimental materialize validate readme pre-sync post-sync pre-validate post-validate _apply-sync-schedule
+.PHONY: print-logo sync sync-experimental validate readme pre-sync post-sync pre-validate post-validate _apply-sync-schedule
 
 # Hook targets (double-colon rules allow multiple definitions)
 # Note: pre-install/post-install are defined in bootstrap.mk
@@ -173,11 +173,6 @@ _apply-sync-schedule: ## (internal) apply RHIZA_SYNC_SCHEDULE override to GitHub
 		printf "${BLUE}[INFO] Applied custom sync schedule: $(RHIZA_SYNC_SCHEDULE)${RESET}\n"; \
 	fi
 
-materialize: ## [DEPRECATED] use 'make sync' instead — materialize --force is now sync
-	@printf "${YELLOW}[WARN] 'make materialize' is deprecated and will be removed in a future release.${RESET}\n"
-	@printf "${YELLOW}[WARN] Please use 'make sync' instead (e.g. 'materialize --force' is now 'make sync').${RESET}\n"
-	@$(MAKE) sync
-
 summarise-sync: install-uv ## summarise differences created by sync with template repository
 	@if [ -n "$(IS_MOTHER_REPO)" ]; then \
 		printf "${BLUE}[INFO] Skipping summarise-sync in rhiza repository (no template.yml by design)${RESET}\n"; \

CHANGELOG.md

@@ -309,17 +309,17 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 - *(models)* Increase test coverage to 100%
 
 ### Other Changes
-- Deprecate the `migrate` command (#377)
+- Deprecate the legacy folder-structure command (#377)
 - Move clone/snapshot logic onto RhizaTemplate; remove redundant _sync_helpers functions (#379)
 - Analysis
 - Remove mypy configuration from pyproject.toml
-- Migrate template helpers from `_sync_helpers` to `RhizaTemplate` private methods (#383)
+- Move template helpers from `_sync_helpers` to `RhizaTemplate` private methods (#383)
 - Remove `rhiza welcome` command (#391)
 - Inline bundle_resolver.py into models.py (#392)
 - Move `get_git_executable` from `subprocess_utils` into `models` (#393)
 - Refactor CLI error handling with `_exit_on_error` context manager (#394)
 - Trim verbose docstring in `commands/__init__.py` (#398)
-- Remove deprecated `materialize` command (#399)
+- Remove deprecated legacy sync command (#399)
 - Standardise YAML serialization behind a shared Protocol and generic helper (#405)
 - Replace stringly-typed `git_host` with `GitHost` StrEnum (#407)
 - Revisit tests: rename test_subprocess_utils.py, split test_models.py, add write_yaml fixture (#411)
@@ -414,8 +414,8 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 - *(sync)* Concurrency-safe lock file I/O with fcntl + atomic rename (#315)
 
 ### Bug Fixes
-- Loosen PyYAML pin and migrate materialize to sync (#303)
-- Migrate rhiza_sync.yml from deprecated `materialize --force` to `rhiza sync` (#305)
+- Loosen PyYAML pin and move the legacy command to sync (#303)
+- Move rhiza_sync.yml from the deprecated legacy command to `rhiza sync` (#305)
 
 ### Documentation
 - Reorder REPOSITORY_ANALYSIS.md newest-first
@@ -432,7 +432,7 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 - Updated REPOSITORY ANALYSIS
 - Initial plan (#301)
 - Delete .rhiza/history (#302)
-- Retire materialize.py: consolidate shared helpers into sync.py (#299)
+- Retire the legacy command module: consolidate shared helpers into sync.py (#299)
 - Validate template repository reachability before writing config in `rhiza init` (#307)
 - Analysis
 - Add rhiza sync smoke test CI workflow (#321)
@@ -485,7 +485,7 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 - Delete orphaned files during sync when template.yml changes (#271)
 
 ### Other Changes
-- Deprecate `materialize` — collapse into `sync` (#273)
+- Deprecate the legacy command — collapse into `sync` (#273)
 - Remove `--strategy overwrite` from `rhiza sync` (#276)
 - Enhance template.lock to structured YAML with full sync metadata (#278)
 - Bump version 0.11.3 → 0.11.4-rc.1
@@ -648,7 +648,7 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 - Add deptry package_module_name_map entries to silence assumption warnings (#178)
 - Achieve 100% statement coverage (#188)
 - Add doctests to resolve test_docstrings skip (#190)
-- Suppress stack traces in materialize command for expected git errors (#169)
+- Suppress stack traces in the sync command for expected git errors (#169)
 - Bump version 0.9.0 → 0.9.1
 
 ## [0.9.0] - 2026-01-18
@@ -752,16 +752,16 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 ## [0.8.1] - 2025-12-26
 
 ### Other Changes
-- Replace init with validate in materialize command (#117)
-- Ensure .rhiza folder is included in template.yml during migration (#119)
+- Replace init with validate in the sync command (#117)
+- Ensure .rhiza folder is included in template.yml during the folder-structure move (#119)
 
 ## [0.8.0] - 2025-12-26
 
 ### Other Changes
 - Add src, tests, and pyproject.toml validation to validate command (#106)
 - Achieve 100% test coverage (#111)
 - Add uninstall command to remove Rhiza-managed files (#109)
-- Add migrate command and update existing commands for .rhiza folder structure (#113)
+- Add .rhiza folder-structure support and update existing commands (#113)
 
 ## [0.7.2] - 2025-12-24
 
@@ -780,7 +780,7 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 ## [0.7.0] - 2025-12-24
 
 ### New Features
-- Auto-cleanup orphaned files during materialize (#95)
+- Auto-cleanup orphaned files during sync (#95)
 
 ### Other Changes
 - Rhiza notebook
@@ -822,7 +822,7 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 
 ### Other Changes
 - Hide expand_paths better (#66)
-- Fix materialize command hanging on sparse checkout operations (#68)
+- Fix sync command hanging on sparse checkout operations (#68)
 
 ## [0.5.4] - 2025-12-18
 
@@ -837,14 +837,14 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 - Better comments
 - Fmt
 - Empty lines for better display
-- [WIP] Add branch option to materialize changes (#62)
+- [WIP] Add branch option to sync changes (#62)
 - Markdown for pdoc?
 - Markdown for pdoc?
 - Markdown for pdoc?
 - Fmt
 - Fmt
 - Fmt
-- Add sym2 workflow for rhiza template materialization from update_rhiza branch (#64)
+- Add sym2 workflow for rhiza template sync from update_rhiza branch (#64)
 
 ## [0.5.3] - 2025-12-18
 
@@ -859,7 +859,7 @@ and entries are generated from [Conventional Commits](https://www.conventionalco
 
 ### Other Changes
 - Don't delete the unused branch?
-- Materialize with rhiza history
+- Sync with rhiza history
 - Rhiza.history
 
 ## [0.5.1] - 2025-12-17

CLI.md

@@ -10,8 +10,6 @@ This document provides a quick reference for the Rhiza command-line interface.
 |---------|-------------|
 | `rhiza init` | Initialize or validate `.rhiza/template.yml` |
 | `rhiza sync` | Sync templates (first-time copy **or** 3-way merge on updates) |
-| `rhiza materialize` | *(Deprecated)* Use `rhiza sync` instead |
-| `rhiza migrate` | Migrate to the new `.rhiza` folder structure |
 | `rhiza validate` | Validate template configuration |
 
 ## Common Usage Patterns
@@ -114,49 +112,6 @@ rhiza sync --target-branch update-templates # Work in a dedicated branch
 
 ---
 
-### rhiza materialize *(Deprecated)*
-
-> **Deprecated.** Use `rhiza sync` instead.
->
-> | Old command | Equivalent new command |
-> |-------------|----------------------|
-> | `rhiza materialize` | `rhiza sync` |
-> | `rhiza materialize --force` | `rhiza sync` |
-
----
-
-### rhiza migrate
-
-**Purpose:** Migrate project to the new `.rhiza` folder structure
-
-**Syntax:**
-```bash
-rhiza migrate [TARGET]
-```
-
-**Parameters:**
-- `TARGET` - Target repository directory (default: current directory)
-
-**Examples:**
-```bash
-rhiza migrate                    # Migrate current directory
-rhiza migrate /path/to/project   # Migrate specific directory
-```
-
-**What It Does:**
-- Creates the `.rhiza/` directory in the project root
-- Moves `template.yml` from `.github/rhiza/` or `.github/` to `.rhiza/template.yml`
-- Moves `.rhiza.history` to `.rhiza/history`
-- Provides instructions for next steps
-- Skips files that already exist in `.rhiza/` (leaves old files in place for manual cleanup)
-
-**When to Use:**
-- Transitioning to the new `.rhiza/` folder structure
-- Organizing Rhiza configuration separately from `.github/`
-- Cleaning up project structure
-
----
-
 ### rhiza validate
 
 **Purpose:** Validate `.rhiza/template.yml` configuration
@@ -213,7 +168,7 @@ It records the full state of the last successful sync as a YAML file, enabling i
 | `include` | Paths included from the template repository |
 | `exclude` | Paths excluded from the template repository |
 | `templates` | Bundle names used (empty when using path-based mode) |
-| `files` | Sorted list of every file materialized in this sync |
+| `files` | Sorted list of every file synced in this sync |
 
 **Example:**
 ```yaml

GETTING_STARTED.md

@@ -8,7 +8,7 @@
 
 Think of it as **an autopilot for syncing hundreds of repos with one or more anchor repositories**. You decide which template repositories act as your anchor repositories — the default `jebel-quant/rhiza`, your organization’s custom templates, your personal hub, or a combination of sources.
 
-When your anchor templates evolve — new workflows, updated linting rules, or security improvements — Rhiza ensures all your projects stay in sync with **a single command** or automatically via scheduled materializations.
+When your anchor templates evolve — new workflows, updated linting rules, or security improvements — Rhiza ensures all your projects stay in sync with **a single command** or automatically via scheduled syncs.
 
 ---
 

README.md

@@ -22,7 +22,7 @@ Command-line interface for managing reusable configuration templates for modern
 Rhiza is a CLI tool that helps you maintain consistent configuration across multiple Python projects by using templates stored in a central repository. It allows you to:
 
 - Initialize projects with standard configuration templates
-- Materialize (inject) templates into target repositories
+- Sync (inject) templates into target repositories
 - Validate template configurations
 - Keep project configurations synchronized with template repositories
 
@@ -34,8 +34,6 @@ Rhiza is a CLI tool that helps you maintain consistent configuration across mult
 - [Commands](#commands)
   - [init](#rhiza-init)
   - [sync](#rhiza-sync)
-  - [materialize](#rhiza-materialize-deprecated) *(deprecated)*
-  - [migrate](#rhiza-migrate)
   - [validate](#rhiza-validate)
 - [Configuration](#configuration)
 - [Examples](#examples)
@@ -312,97 +310,6 @@ rhiza sync --target-branch update-templates
 
 ---
 
-### `rhiza materialize` *(Deprecated)*
-
-> **Deprecated.** Use `rhiza sync` instead.
-
-| Old command | Equivalent new command |
-|-------------|----------------------|
-| `rhiza materialize` | `rhiza sync` |
-| `rhiza materialize --force` | `rhiza sync` |
-
----
-
-### `rhiza migrate`
-
-Migrate project to the new `.rhiza` folder structure.
-
-**Usage:**
-
-```bash
-rhiza migrate [OPTIONS] [TARGET]
-```
-
-**Arguments:**
-
-- `TARGET` - Target git repository directory (defaults to current directory)
-
-**Arguments:**
-
-- `TARGET` - Target git repository directory (defaults to current directory)
-
-**Description:**
-
-Migrates your project to use the new `.rhiza/` folder structure for storing Rhiza state and configuration files. This command helps transition from the old structure where configuration was stored in `.github/rhiza/` and `.rhiza.history` in the project root.
-
-The migration performs the following actions:
-
-1. Creates the `.rhiza/` directory in the project root
-2. Moves `template.yml` from `.github/rhiza/` or `.github/` to `.rhiza/template.yml`
-3. Moves `.rhiza.history` to `.rhiza/history`
-4. Provides instructions for next steps
-
-The new `.rhiza/` folder structure provides better organization by separating Rhiza's state and configuration from the `.github/` directory.
-
-**Examples:**
-
-```bash
-# Migrate current directory
-rhiza migrate
-
-# Migrate a specific directory
-rhiza migrate /path/to/project
-```
-
-**Output:**
-
-```
-[INFO] Migrating Rhiza structure in: /path/to/project
-[INFO] This will create the .rhiza folder and migrate configuration files
-[INFO] Creating .rhiza directory at: .rhiza
-✓ Created .rhiza
-[INFO] Found template.yml at: .rhiza/template.yml
-[INFO] Moving to new location: .rhiza/template.yml
-✓ Moved template.yml to .rhiza/template.yml
-✓ Migration completed successfully
-
-Migration Summary:
-  - Created .rhiza/ folder
-  - Moved template.yml to .rhiza/template.yml
-  - Moved history tracking to .rhiza/history
-
-Next steps:
-  1. Review changes:
-       git status
-       git diff
-
-  2. Update other commands to use new .rhiza/ location
-     (Future rhiza versions will automatically use .rhiza/)
-
-  3. Commit the migration:
-       git add .
-       git commit -m "chore: migrate to .rhiza folder structure"
-```
-
-**Notes:**
-
-- If files already exist in `.rhiza/`, the migration will skip them and leave the old files in place
-- You can manually remove old files after verifying the migration was successful
-- The old `.rhiza.history` file is removed after successful migration to `.rhiza/history`
-- The original template file in `.github/` is moved (removed from old location)
-
----
-
 ### `rhiza validate`
 
 Validate Rhiza template configuration.
@@ -875,7 +782,6 @@ src/rhiza/
 └── commands/           # Command implementations
     ├── __init__.py
     ├── init.py         # Initialize template.yml
-    ├── materialize.py  # Shared helpers (used by sync.py)
     ├── sync.py         # Sync templates (primary command)
     └── validate.py     # Validate configuration
 ```