feat!: remove legacy --ai, --ai-commands-dir, and --ai-skills flags (0.10.0) (#2872)

* Initial plan

* feat!: remove legacy --ai, --ai-commands-dir, and --ai-skills flags at 0.10.0

* refactor(tests): rename stale test_ai_help_* methods to test_agent_config_*

* fix: address review — derive agent folder for generic integration and remove redundant test

- Security notice now falls back to integration_parsed_options['commands_dir']
  when AGENT_CONFIG folder is None (generic integration).
- Remove test_agent_config_includes_kiro_cli which duplicates the assertion
  in test_runtime_config_uses_kiro_cli_and_removes_q.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* docs: scrub all remaining --ai flag references from source and tests

- Remove dead AI_ASSISTANT_ALIASES, AI_ASSISTANT_HELP, and
  _build_ai_assistant_help() from _agent_config.py
- Update comments/docstrings in extensions.py, presets.py, and
  integration subpackages to reference 'skills mode' or
  '--integration' instead of the removed flags
- Fix catalog.json generic integration description
- Update test docstrings/comments in test_extension_skills.py,
  test_extensions.py, and test_presets.py

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* test: remove legacy --ai flag rejection tests

The flags are fully removed from the CLI; typer handles unknown options
generically. No custom rejection logic exists to test.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* revert: remove manual CHANGELOG.md entry

CHANGELOG is generated automatically; manual edits should not be made.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: make generic catalog description self-explanatory

Include the required --commands-dir sub-option in the description so
readers don't need to look up integration docs.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(tests): rename duplicate test classes to avoid shadowing

The rename from Test*AutoPromote to Test*Integration collided with the
existing Test*Integration(SkillsIntegrationTests) base classes, causing
the shared test suites to be silently overwritten. Rename the CLI init
flow classes to Test*InitFlow instead.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <mnriem@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: 3 people

integrations/catalog.json

@@ -277,7 +277,7 @@
       "id": "generic",
       "name": "Generic (bring your own agent)",
       "version": "1.0.0",
-      "description": "Generic integration for any agent via --ai-commands-dir",
+      "description": "Generic integration for any agent via --integration-options=\"--commands-dir <dir>\"",
       "author": "spec-kit-core",
       "repository": "https://github.com/github/spec-kit",
       "tags": ["generic"]

src/specify_cli/__init__.py

@@ -82,8 +82,6 @@
 )
 from ._agent_config import (
     AGENT_CONFIG as AGENT_CONFIG,
-    AI_ASSISTANT_ALIASES as AI_ASSISTANT_ALIASES,
-    AI_ASSISTANT_HELP as AI_ASSISTANT_HELP,
     DEFAULT_INIT_INTEGRATION as DEFAULT_INIT_INTEGRATION,
     SCRIPT_TYPE_CHOICES as SCRIPT_TYPE_CHOICES,
 )

src/specify_cli/_agent_config.py

@@ -17,29 +17,4 @@ def _build_agent_config() -> dict[str, dict[str, Any]]:
 
 DEFAULT_INIT_INTEGRATION = "copilot"
 
-AI_ASSISTANT_ALIASES: dict[str, str] = {
-    "kiro": "kiro-cli",
-}
-
-
-def _build_ai_assistant_help() -> str:
-    non_generic_agents = sorted(agent for agent in AGENT_CONFIG if agent != "generic")
-    base_help = (
-        f"AI assistant to use: {', '.join(non_generic_agents)}, "
-        "or generic (requires --ai-commands-dir)."
-    )
-    if not AI_ASSISTANT_ALIASES:
-        return base_help
-    alias_phrases = []
-    for alias, target in sorted(AI_ASSISTANT_ALIASES.items()):
-        alias_phrases.append(f"'{alias}' as an alias for '{target}'")
-    if len(alias_phrases) == 1:
-        aliases_text = alias_phrases[0]
-    else:
-        aliases_text = ", ".join(alias_phrases[:-1]) + " and " + alias_phrases[-1]
-    return base_help + " Use " + aliases_text + "."
-
-
-AI_ASSISTANT_HELP: str = _build_ai_assistant_help()
-
 SCRIPT_TYPE_CHOICES: dict[str, str] = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}

src/specify_cli/commands/init.py

@@ -2,7 +2,6 @@
 from __future__ import annotations
 
 import os
-import shlex
 import shutil
 import sys
 from pathlib import Path
@@ -14,8 +13,6 @@
 
 from .._agent_config import (
     AGENT_CONFIG,
-    AI_ASSISTANT_ALIASES,
-    AI_ASSISTANT_HELP,
     DEFAULT_INIT_INTEGRATION,
     SCRIPT_TYPE_CHOICES,
 )
@@ -28,31 +25,6 @@
 from .._console import StepTracker, console, select_with_arrows, show_banner
 from .._utils import check_tool, init_git_repo, is_git_repo
 
-def _build_integration_equivalent(
-    integration_key: str,
-    ai_commands_dir: str | None = None,
-) -> str:
-    parts = [f"--integration {integration_key}"]
-    if integration_key == "generic" and ai_commands_dir:
-        parts.append(
-            f'--integration-options="--commands-dir {shlex.quote(ai_commands_dir)}"'
-        )
-    return " ".join(parts)
-
-
-def _build_ai_deprecation_warning(
-    integration_key: str,
-    ai_commands_dir: str | None = None,
-) -> str:
-    replacement = _build_integration_equivalent(
-        integration_key,
-        ai_commands_dir=ai_commands_dir,
-    )
-    return (
-        "[bold]--ai[/bold] is deprecated and will no longer be available in version 0.10.0 or later.\n\n"
-        f"Use [bold]{replacement}[/bold] instead."
-    )
-
 
 def _stdin_is_interactive() -> bool:
     return sys.stdin.isatty()
@@ -97,8 +69,6 @@ def register(app: typer.Typer) -> None:
     @app.command()
     def init(
         project_name: str = typer.Argument(None, help="Name for your new project directory (optional if using --here, or use '.' for current directory)"),
-        ai_assistant: str = typer.Option(None, "--ai", help=AI_ASSISTANT_HELP),
-        ai_commands_dir: str = typer.Option(None, "--ai-commands-dir", help="Directory for agent command files (required with --ai generic, e.g. .myagent/commands/)"),
         script_type: str = typer.Option(None, "--script", help="Script type to use: sh or ps"),
         ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for coding agent tools like Claude Code"),
         no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
@@ -107,11 +77,10 @@ def init(
         skip_tls: bool = typer.Option(False, "--skip-tls", help="Deprecated (no-op). Previously: skip SSL/TLS verification.", hidden=True),
         debug: bool = typer.Option(False, "--debug", help="Deprecated. Previously: show verbose diagnostic output; currently only prints additional diagnostic details on failure.", hidden=True),
         github_token: str = typer.Option(None, "--github-token", help="Deprecated (no-op). Previously: GitHub token for API requests.", hidden=True),
-        ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
         offline: bool = typer.Option(False, "--offline", help="Deprecated (no-op). All scaffolding now uses bundled assets.", hidden=True),
         preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
         branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, …, 1000, … — expands past 999 automatically) or 'timestamp' (YYYYMMDD-HHMMSS)"),
-        integration: str = typer.Option(None, "--integration", help="Use the new integration system (e.g. --integration copilot). Mutually exclusive with --ai."),
+        integration: str = typer.Option(None, "--integration", help="AI coding agent integration to use (e.g. --integration copilot). See 'specify check' for available integrations."),
         integration_options: str = typer.Option(None, "--integration-options", help='Options for the integration (e.g. --integration-options="--commands-dir .myagent/cmds")'),
     ):
         """
@@ -163,27 +132,6 @@ def init(
         from ..integration_runtime import with_integration_setting as _with_integration_setting
 
         show_banner()
-        ai_deprecation_warning: str | None = None
-
-        if ai_assistant and ai_assistant.startswith("--"):
-            console.print(f"[red]Error:[/red] Invalid value for --ai: '{ai_assistant}'")
-            console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai?")
-            console.print("[yellow]Example:[/yellow] specify init --integration claude --here")
-            console.print(f"[yellow]Available agents:[/yellow] {', '.join(AGENT_CONFIG.keys())}")
-            raise typer.Exit(1)
-
-        if ai_commands_dir and ai_commands_dir.startswith("--"):
-            console.print(f"[red]Error:[/red] Invalid value for --ai-commands-dir: '{ai_commands_dir}'")
-            console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai-commands-dir?")
-            console.print("[yellow]Example:[/yellow] specify init --integration generic --integration-options=\"--commands-dir .myagent/commands/\"")
-            raise typer.Exit(1)
-
-        if ai_assistant:
-            ai_assistant = AI_ASSISTANT_ALIASES.get(ai_assistant, ai_assistant)
-
-        if integration and ai_assistant:
-            console.print("[red]Error:[/red] --integration and --ai are mutually exclusive")
-            raise typer.Exit(1)
 
         from ..integrations import INTEGRATION_REGISTRY, get_integration
         if integration:
@@ -193,35 +141,6 @@ def init(
                 available = ", ".join(sorted(INTEGRATION_REGISTRY))
                 console.print(f"[yellow]Available integrations:[/yellow] {available}")
                 raise typer.Exit(1)
-            ai_assistant = integration
-        elif ai_assistant:
-            resolved_integration = get_integration(ai_assistant)
-            if not resolved_integration:
-                console.print(f"[red]Error:[/red] Unknown agent '{ai_assistant}'. Choose from: {', '.join(sorted(INTEGRATION_REGISTRY))}")
-                raise typer.Exit(1)
-            ai_deprecation_warning = _build_ai_deprecation_warning(
-                resolved_integration.key,
-                ai_commands_dir=ai_commands_dir,
-            )
-
-        if ai_assistant or integration:
-            if ai_skills:
-                from ..integrations.base import SkillsIntegration as _SkillsCheck
-                if isinstance(resolved_integration, _SkillsCheck):
-                    console.print(
-                        "[dim]Note: --ai-skills is not needed; "
-                        "skills are the default for this integration.[/dim]"
-                    )
-                else:
-                    console.print(
-                        "[dim]Note: --ai-skills has no effect with "
-                        f"{resolved_integration.key}; this integration uses commands, not skills.[/dim]"
-                    )
-            if ai_commands_dir and resolved_integration.key != "generic":
-                console.print(
-                    "[dim]Note: --ai-commands-dir is deprecated; "
-                    'use [bold]--integration generic --integration-options="--commands-dir <dir>"[/bold] instead.[/dim]'
-                )
 
         if no_git:
             console.print(
@@ -242,11 +161,6 @@ def init(
             console.print("[red]Error:[/red] Must specify either a project name, use '.' for current directory, or use --here flag")
             raise typer.Exit(1)
 
-        if ai_skills and not ai_assistant:
-            console.print("[red]Error:[/red] --ai-skills requires --ai to be specified")
-            console.print("[yellow]Usage:[/yellow] specify init <project> --ai <agent> --ai-skills")
-            raise typer.Exit(1)
-
         BRANCH_NUMBERING_CHOICES = {"sequential", "timestamp"}
         if branch_numbering and branch_numbering not in BRANCH_NUMBERING_CHOICES:
             console.print(f"[red]Error:[/red] Invalid --branch-numbering value '{branch_numbering}'. Choose from: {', '.join(sorted(BRANCH_NUMBERING_CHOICES))}")
@@ -295,11 +209,11 @@ def init(
                     console.print(error_panel)
                     raise typer.Exit(1)
 
-        if ai_assistant:
-            if ai_assistant not in AGENT_CONFIG:
-                console.print(f"[red]Error:[/red] Invalid AI assistant '{ai_assistant}'. Choose from: {', '.join(AGENT_CONFIG.keys())}")
+        if integration:
+            if integration not in AGENT_CONFIG:
+                console.print(f"[red]Error:[/red] Invalid integration '{integration}'. Choose from: {', '.join(AGENT_CONFIG.keys())}")
                 raise typer.Exit(1)
-            selected_ai = ai_assistant
+            selected_ai = integration
         elif not _stdin_is_interactive():
             console.print(
                 f"[dim]Non-interactive session detected: defaulting to '{DEFAULT_INIT_INTEGRATION}'. "
@@ -314,17 +228,16 @@ def init(
                 DEFAULT_INIT_INTEGRATION,
             )
 
-        if not ai_assistant:
+        if not integration:
             resolved_integration = get_integration(selected_ai)
             if not resolved_integration:
                 console.print(f"[red]Error:[/red] Unknown agent '{selected_ai}'")
                 raise typer.Exit(1)
 
         if selected_ai == "generic" and not integration_options:
-            if not ai_commands_dir:
-                console.print("[red]Error:[/red] --ai-commands-dir is required when using --ai generic or --integration generic")
-                console.print('[dim]Example: specify init my-project --integration generic --integration-options="--commands-dir .myagent/commands/"[/dim]')
-                raise typer.Exit(1)
+            console.print("[red]Error:[/red] --integration generic requires --integration-options with --commands-dir")
+            console.print('[dim]Example: specify init my-project --integration generic --integration-options="--commands-dir .myagent/commands/"[/dim]')
+            raise typer.Exit(1)
 
         current_dir = Path.cwd()
 
@@ -414,10 +327,6 @@ def init(
                 )
 
                 integration_parsed_options: dict[str, Any] = {}
-                if ai_commands_dir:
-                    integration_parsed_options["commands_dir"] = ai_commands_dir
-                if ai_skills:
-                    integration_parsed_options["skills"] = True
                 if integration_options:
                     extra = _parse_integration_options(resolved_integration, integration_options)
                     if extra:
@@ -675,7 +584,7 @@ def init(
 
         agent_config = AGENT_CONFIG.get(selected_ai)
         if agent_config:
-            agent_folder = ai_commands_dir if selected_ai == "generic" else agent_config["folder"]
+            agent_folder = agent_config["folder"] or integration_parsed_options.get("commands_dir")
             if agent_folder:
                 security_notice = Panel(
                     f"Some agents may store credentials, auth tokens, or other identifying and private artifacts in the agent folder within your project.\n"
@@ -687,16 +596,6 @@ def init(
                 console.print()
                 console.print(security_notice)
 
-        if ai_deprecation_warning:
-            deprecation_notice = Panel(
-                ai_deprecation_warning,
-                title="[bold red]Deprecation Warning[/bold red]",
-                border_style="red",
-                padding=(1, 2),
-            )
-            console.print()
-            console.print(deprecation_notice)
-
         if git_default_notice:
             default_change_notice = Panel(
                 "The git extension is currently enabled by default during [bold]specify init[/bold].\n"
@@ -720,24 +619,24 @@ def init(
         from ..integrations.base import SkillsIntegration as _SkillsInt
         _is_skills_integration = isinstance(resolved_integration, _SkillsInt) or getattr(resolved_integration, "_skills_mode", False)
 
-        codex_skill_mode = selected_ai == "codex" and (ai_skills or _is_skills_integration)
-        claude_skill_mode = selected_ai == "claude" and (ai_skills or _is_skills_integration)
+        codex_skill_mode = selected_ai == "codex" and _is_skills_integration
+        claude_skill_mode = selected_ai == "claude" and _is_skills_integration
         kimi_skill_mode = selected_ai == "kimi"
         agy_skill_mode = selected_ai == "agy" and _is_skills_integration
         trae_skill_mode = selected_ai == "trae"
-        cursor_agent_skill_mode = selected_ai == "cursor-agent" and (ai_skills or _is_skills_integration)
+        cursor_agent_skill_mode = selected_ai == "cursor-agent" and _is_skills_integration
         copilot_skill_mode = selected_ai == "copilot" and _is_skills_integration
         devin_skill_mode = selected_ai == "devin"
         cline_skill_mode = selected_ai == "cline"
         native_skill_mode = codex_skill_mode or claude_skill_mode or kimi_skill_mode or agy_skill_mode or trae_skill_mode or cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode
 
-        if codex_skill_mode and not ai_skills:
+        if codex_skill_mode:
             steps_lines.append(f"{step_num}. Start Codex in this project directory; spec-kit skills were installed to [cyan].agents/skills[/cyan]")
             step_num += 1
-        if claude_skill_mode and not ai_skills:
+        if claude_skill_mode:
             steps_lines.append(f"{step_num}. Start Claude in this project directory; spec-kit skills were installed to [cyan].claude/skills[/cyan]")
             step_num += 1
-        if cursor_agent_skill_mode and not ai_skills:
+        if cursor_agent_skill_mode:
             steps_lines.append(f"{step_num}. Start Cursor Agent in this project directory; spec-kit skills were installed to [cyan].cursor/skills[/cyan]")
             step_num += 1
         if devin_skill_mode:

src/specify_cli/extensions.py

@@ -889,7 +889,7 @@ def _register_extension_skills(
 
         For every command in the extension manifest, creates a SKILL.md
         file in the agent's skills directory following the agentskills.io
-        specification.  This is only done when ``--ai-skills`` was used
+        specification.  This is only done when skills mode was used
         during project initialisation.
 
         Args:
@@ -1295,7 +1295,7 @@ def install_from_directory(
                 create_missing_active_skills_dir=True,
             )
 
-        # Auto-register extension commands as agent skills when --ai-skills
+        # Auto-register extension commands as agent skills when skills mode
         # was used during project initialisation (feature parity).
         registered_skills = self._register_extension_skills(
             manifest, dest_dir, link_outputs=link_commands

src/specify_cli/integrations/cursor_agent/__init__.py

@@ -22,7 +22,7 @@ class CursorAgentIntegration(SkillsIntegration):
         "folder": ".cursor/",
         "commands_subdir": "skills",
         "install_url": "https://docs.cursor.com/en/cli/overview",
-        # IDE-first integration: ``specify init --ai cursor-agent`` must
+        # IDE-first integration: ``specify init --integration cursor-agent`` must
         # work without the ``cursor-agent`` CLI installed (the IDE flow
         # uses skills directly).  Workflow dispatch additionally requires
         # the CLI on PATH, but that's enforced at dispatch time via

src/specify_cli/integrations/hermes/__init__.py

@@ -7,7 +7,7 @@
 Usage::
 
     specify init my-project --integration hermes
-    specify init --here --ai hermes
+    specify init --here --integration hermes
 """
 
 from __future__ import annotations

src/specify_cli/presets.py

@@ -1219,7 +1219,7 @@ def _register_skills(
         directory.  If so, the skill is overwritten with content derived
         from the preset's command file.  This ensures that presets that
         override commands also propagate to the agentskills.io skill
-        layer when ``--ai-skills`` was used during project initialisation.
+        layer when skills mode was used during project initialisation.
 
         Args:
             manifest: Preset manifest.
@@ -1559,7 +1559,7 @@ def install_from_directory(
                 "registered_commands": registered_commands,
             })
 
-            # Update corresponding skills when --ai-skills was previously used
+            # Update corresponding skills when skills mode was previously used
             # and persist that result as well.
             registered_skills = self._register_skills(manifest, dest_dir)
             self.registry.update(manifest.id, {