[Bug]: bundle init <bundle> initialises with the default integration instead of the bundle's, then aborts with a clash #5089

Bug Description

In a directory that is not yet a Spec Kit project, specify bundle init <bundle> picks the init integration with _resolve_init_integration(integration, None) (src/specify_cli/bundles/command_init.py:33). Because it passes None instead of the manifest, it skips the bundle-declared integration and initialises the project with the default (copilot). The follow-up install then fails because the bundle targets a different integration.

The project is left initialised with the wrong integration, although the error message says "aborting with no changes". specify bundle install <bundle> in the same situation passes the manifest (command_install.py:98) and initialises with the bundle's integration.

Steps to Reproduce

From the root of a fresh clone after uv sync, save the script below as repro.py and run uv run python -I repro.py. It runs the real specify CLI with --offline. No network access is needed, and HOME points at the temp directory so user configuration is not read.

import json, os, subprocess, tempfile
from pathlib import Path

work = Path(tempfile.mkdtemp())
bundle = work / "claude-bundle"; bundle.mkdir()
(bundle / "bundle.yml").write_text(
    'schema_version: "1.0"\n'
    'bundle: {id: claude-bundle, name: C, version: "1.0.0", role: dev, description: d, author: a, license: MIT}\n'
    'requires: {speckit_version: ">=0.0.1"}\n'
    'integration: {id: claude}\n'
)
env = {"PATH": os.environ["PATH"], "HOME": str(work), "COLUMNS": "200"}

for command in (["bundle", "install"], ["bundle", "init"]):
    project = work / command[1]; project.mkdir()
    run = subprocess.run(["specify", *command, str(bundle), "--offline"],
                         cwd=project, capture_output=True, text=True, env=env)
    state = project / ".specify" / "integration.json"
    integration = json.loads(state.read_text())["default_integration"] if state.exists() else None
    errors = [line for line in (run.stdout + run.stderr).splitlines() if "Error" in line]
    print(f"specify {' '.join(command)}: exit {run.returncode}, project integration={integration}, "
          f"bundle recorded={(project / '.specify' / 'bundle-records.json').exists()}")
    for line in errors:
        print("   ", line)

Expected Behavior

bundle init <bundle> should behave like bundle install <bundle> and initialise with the bundle's declared integration (claude):

• src/specify_cli/bundles/_commands.py:132: "Precedence (FR-013): explicit override → bundle-declared → default."
• docs/reference/bundles.md:192 describes bundle init as "an explicit one-step bootstrap for a new checkout".
• docs/reference/bundles.md:77: if a bundle targets a different integration, install "aborts with no changes".

Actual Behavior

specify bundle install: exit 0, project integration=claude, bundle recorded=True
specify bundle init: exit 1, project integration=copilot, bundle recorded=False
    Error: Bundle 'claude-bundle' targets integration 'claude', but this project's active integration is 'copilot'. Installing it would conflict; aborting with no changes.

After the failed bundle init, .specify/integration.json records copilot, and the project has been scaffolded for it.

Error Logs

Error: Bundle 'claude-bundle' targets integration 'claude', but this project's active integration is 'copilot'. Installing it would conflict; aborting with no changes.

Specify CLI Version

1.2.4.dev0 (main at 27d14e2)

AI Agent

Claude Code

Operating System

Linux 6.18 (Ubuntu container)

Python Version

Python 3.12.3

Additional Context

Passing --integration claude explicitly avoids the problem. A likely fix is for bundle init to load the bundle's manifest before initialising, as bundle install does.

Also reproduced on macOS (Darwin 25.6, arm64) with Python 3.14.4 and uv run python -I repro.py against 27d14e2; the output matches the above.

AI Disclosure

Found and reproduced with Claude Code (model: Claude Opus 4.8), run autonomously under human supervision. The human reporter re-ran every reproduction above before filing.