refactor: organize extension CLI commands

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Author: mnriem

AGENTS.md

@@ -8,6 +8,14 @@
 
 The toolkit supports multiple AI coding assistants, allowing teams to use their preferred tools while maintaining consistent project structure and development practices.
 
+## Repository Design References
+
+Before adding or reorganizing Specify CLI commands, read
+[Specify CLI Command Architecture](design/cli.md). It defines command-module
+naming, private command phases, nested command groups, registration ownership,
+mirrored tests, and the rationale for making the CLI structure predictable for
+both humans and coding agents.
+
 ---
 
 ## Quickstart — Add a New Integration in 5 Steps

design/cli.md

@@ -0,0 +1,304 @@
+# Specify CLI Command Architecture
+
+This document defines the target structure for multi-command groups in the
+Specify Python CLI. It explains where command handlers, shared infrastructure,
+command-private phases, nested command groups, and their tests belong.
+
+`src/specify_cli/extensions/` is the reference implementation. Apply this
+design incrementally when adding or refactoring other command groups; do not
+create extra modules merely to make a small command conform visually.
+
+## Design goals
+
+The CLI structure should make the answer to "where does this command live?"
+predictable from the command line itself.
+
+The design optimizes for:
+
+- **Direct navigation:** a command maps to an obvious source file and test.
+- **Small working context:** changing one command should not require loading an
+  entire command group into memory.
+- **Parallel development:** unrelated commands should rarely require edits to
+  the same file.
+- **Explicit ownership:** shared infrastructure and command-private behavior
+  should not be mixed.
+- **Stable behavior:** structural refactoring must preserve registration,
+  output, error handling, compatibility paths, and tests.
+- **Agentic development:** coding agents should be able to infer the relevant
+  files from the CLI surface without broad repository searches.
+
+## Naming and ownership
+
+### Registered command modules
+
+Each real CLI command uses:
+
+```text
+command_<name>.py
+```
+
+For example:
+
+```text
+specify extension add           -> extensions/command_add.py
+specify extension set-priority  -> extensions/command_set_priority.py
+specify extension update        -> extensions/command_update.py
+```
+
+Only modules representing actual CLI commands use the non-underscored
+`command_*.py` prefix. A command module owns:
+
+- The Typer-decorated handler.
+- User-facing arguments and options.
+- Command-specific orchestration.
+- Small helpers used only by that command.
+
+The command function's docstring is user-facing because Typer may display it
+as help text. A module docstring is internal and should identify the command,
+registration path, and any adjacent private implementation modules.
+
+### Command-private implementation modules
+
+When a command has cohesive phases that are independently understandable or
+testable, use:
+
+```text
+_command_<name>_<phase>.py
+```
+
+For example:
+
+```text
+command_update.py
+_command_update_discovery.py
+_command_update_artifacts.py
+_command_update_transaction.py
+```
+
+The leading underscore marks the module as private implementation. The
+`command_update` portion groups it with the registered handler in searches and
+file listings. The phase suffix communicates its ownership.
+
+Private phase modules must not register additional CLI commands. The public
+`command_<name>.py` module remains the sole CLI adapter.
+
+Split a command when a phase:
+
+- Has distinct invariants or failure behavior.
+- Can be tested as a meaningful boundary.
+- Has enough implementation detail to distract from the CLI handler.
+- Is likely to change independently from other phases.
+
+Do not split a command solely because it crossed an arbitrary line count.
+Excessive fragmentation makes control flow harder to follow and increases the
+number of files an agent must inspect.
+
+### Command-group infrastructure
+
+For a multi-command group, `_commands.py` owns:
+
+- The command group's Typer application.
+- Registration of the group's command modules.
+- Infrastructure genuinely shared by multiple commands or external CLI flows.
+- Thin compatibility forwarders needed to preserve established import or
+  monkeypatch paths.
+
+`_commands.py` must not contain decorated command handlers. A helper used by
+only one command belongs in that command's module or one of its private phase
+modules.
+
+Compatibility forwarders do not transfer ownership back to `_commands.py`.
+They should remain thin and delegate to the module that owns the behavior.
+Avoid turning `_commands.py` into a service locator for new code.
+
+### Package `__init__.py`
+
+The package `__init__.py` owns the package's domain API and package-level
+behavior. It should provide a brief map to the CLI modules, but it is not the
+home for command handlers.
+
+Moving command handlers out of `__init__.py` keeps importing the domain package
+separate from understanding or modifying its CLI surface.
+
+## Nested command groups
+
+Nested CLI groups use directories matching the command surface:
+
+```text
+specify extension catalog add
+                          list
+                          remove
+```
+
+maps to:
+
+```text
+extensions/
+├── catalog/
+│   ├── __init__.py
+│   ├── _helpers.py
+│   ├── command_add.py
+│   ├── command_list.py
+│   └── command_remove.py
+├── command_add.py
+├── command_list.py
+└── ...
+```
+
+The nested package's `__init__.py` owns its Typer application and registration.
+Shared helpers for that nested surface can live in `_helpers.py`.
+
+Do not add a nested `_commands.py` merely for symmetry. Create one only when
+the nested group develops substantial shared command infrastructure that no
+longer fits cleanly in `__init__.py` and `_helpers.py`.
+
+Do not create a nested directory for an implementation phase that is not a CLI
+subcommand. For example, an `update/` directory would incorrectly suggest an
+`extension update ...` subcommand group. Use `_command_update_<phase>.py`
+instead.
+
+## Registration
+
+Command registration remains centralized at the command-group boundary.
+
+For the extension group:
+
+1. `src/specify_cli/extensions/_commands.py` owns `extension_app`.
+2. `_commands.register()` registers the nested catalog group.
+3. It imports each `command_*.py` module so its decorator registers the
+   handler.
+4. It attaches `extension_app` to the root application.
+
+The nested catalog group follows the same pattern through
+`catalog.register()`.
+
+Registration imports should be explicit and ordered consistently. Do not rely
+on filesystem discovery to import arbitrary modules, because command exposure
+should remain reviewable in one place.
+
+## Test structure
+
+Command-focused tests mirror the source command surface under
+`tests/specify_cli/`.
+
+For example:
+
+```text
+src/specify_cli/extensions/command_add.py
+tests/specify_cli/extensions/test_command_add.py
+
+src/specify_cli/extensions/catalog/command_add.py
+tests/specify_cli/extensions/catalog/test_command_add.py
+```
+
+Private phases use:
+
+```text
+src/specify_cli/extensions/_command_update_discovery.py
+tests/specify_cli/extensions/test_command_update_discovery.py
+
+src/specify_cli/extensions/_command_update_artifacts.py
+tests/specify_cli/extensions/test_command_update_artifacts.py
+
+src/specify_cli/extensions/_command_update_transaction.py
+tests/specify_cli/extensions/test_command_update_transaction.py
+```
+
+The primary `test_command_<name>.py` suite verifies the public command surface.
+Phase-specific suites verify detailed invariants without obscuring the primary
+command behavior.
+
+Not every test belongs in the mirrored command tree:
+
+- Domain model, registry, manager, and catalog behavior remains in domain test
+  suites such as `tests/test_extensions.py`.
+- Cross-domain CLI contracts remain with the broader integration tests.
+- Shared fixtures belong in the narrowest `conftest.py` that serves all of
+  their consumers.
+- Test helpers should be shared rather than copied when both command and domain
+  tests depend on the same behavior.
+
+Moving tests must preserve coverage rather than duplicating it. Run both the
+new command-focused suites and the legacy suites from which tests were moved.
+
+## Reference layout
+
+The extension command group currently demonstrates the complete pattern:
+
+```text
+src/specify_cli/extensions/
+├── __init__.py
+├── _commands.py
+├── command_add.py
+├── command_disable.py
+├── command_enable.py
+├── command_info.py
+├── command_list.py
+├── command_remove.py
+├── command_search.py
+├── command_set_priority.py
+├── command_update.py
+├── _command_update_discovery.py
+├── _command_update_artifacts.py
+├── _command_update_transaction.py
+└── catalog/
+    ├── __init__.py
+    ├── _helpers.py
+    ├── command_add.py
+    ├── command_list.py
+    └── command_remove.py
+```
+
+The update command illustrates the distinction:
+
+- `command_update.py` is the registered CLI adapter.
+- `_command_update_discovery.py` determines available updates.
+- `_command_update_artifacts.py` prepares and validates update archives.
+- `_command_update_transaction.py` owns backup, installation, rollback, and
+  cleanup behavior.
+
+## Decision guide
+
+When deciding where code belongs:
+
+| Question | Location |
+|---|---|
+| Does it define a real CLI command? | `command_<name>.py` |
+| Is it used only by one small command? | That command module |
+| Is it a cohesive private phase of one complex command? | `_command_<name>_<phase>.py` |
+| Is it shared by multiple commands or an external CLI flow? | `_commands.py` or a focused shared module |
+| Does it define a nested CLI namespace? | A directory matching that namespace |
+| Is it shared only by commands in a nested namespace? | The nested package's `_helpers.py` |
+| Is it domain behavior independent of the CLI? | The package domain modules, not command modules |
+
+## Anti-patterns
+
+Avoid:
+
+- Adding decorated handlers back to `_commands.py` or package `__init__.py`.
+- Naming a private implementation module `command_*.py`.
+- Creating nested directories that do not correspond to CLI namespaces.
+- Creating `_commands.py` files only for visual symmetry.
+- Moving command-private helpers into shared infrastructure preemptively.
+- Duplicating fixtures or helpers to make tests appear more mirrored.
+- Splitting a linear function into many files without cohesive phase
+  boundaries.
+- Changing established monkeypatch or import paths without either migrating
+  their consumers or preserving a thin compatibility forwarder.
+
+## Review checklist
+
+For a new or refactored command:
+
+- [ ] The CLI path maps predictably to a `command_<name>.py` module.
+- [ ] Only the real command module registers a handler.
+- [ ] Private phase modules use `_command_<name>_<phase>.py`.
+- [ ] `_commands.py` contains only group infrastructure and genuinely shared
+      behavior.
+- [ ] Nested directories correspond to real CLI namespaces.
+- [ ] Command tests mirror the source structure.
+- [ ] Domain and cross-domain tests remain in their appropriate suites.
+- [ ] Compatibility paths and user-visible help remain unchanged unless the
+      change explicitly requires otherwise.
+- [ ] Focused tests, relevant legacy suites, lint, and the full test suite pass.
+

src/specify_cli/extensions/__init__.py

@@ -4,6 +4,10 @@
 Handles installation, removal, and management of Spec Kit extensions.
 Extensions are modular packages that add commands and functionality to spec-kit
 without bloating the core framework.
+
+CLI handlers live in ``command_*.py`` modules, registered through
+``_commands.py``. Command-private phases use ``_command_<name>_*.py``;
+nested catalog handlers live under ``catalog/``.
 """
 
 from __future__ import annotations