fix(bundles): don't refresh installed components on a repeated bundle init

[kartsan03]

Description

Running specify bundle init <bundle> a second time refreshes the bundle's components that are already installed, even though bundle init has no --refresh option. A local edit to an installed workflow is silently replaced, and the command exits 0.

bundle_init calls the Typer-decorated bundle_install() directly (src/specify_cli/bundles/command_init.py:51 on main) without passing refresh. So refresh keeps its parameter default, typer.Option(False, ...), which is an OptionInfo object and truthy. install_bundle then takes the explicit-refresh path (installer.py:119, :175). It's the same option-default pitfall #4284 fixed for the workflow_add call. The same truthy value also lets bundle init accept a changed bundle version that a plain bundle install refuses without --refresh.

This PR passes refresh=False explicitly from bundle_init. Direct bundle install and bundle install --refresh are unchanged. docs/reference/bundles.md gets one paragraph: repeating bundle init keeps installed components as they are, and bundle update / bundle install --refresh are the ways to refresh them.

Repro with the first-party bugfix bundle, offline: init, append a line to .specify/workflows/bugfix/workflow.yml, init again.

After the second specify bundle init bundles/bugfix --offline	main (3238fa9)	This PR
Install summary	0 added, 0 already present, 2 refreshed, 0 removed	0 added, 2 already present
Local edit to workflow.yml	gone	kept

Testing

• Tested locally with uv run specify --help
• Ran existing tests with uv sync && uv run pytest
• Tested with a sample project (if applicable)

New tests in tests/specify_cli/bundles/test_command_init.py:

• bundle_init delegates to bundle_install with refresh=False (and doesn't call it without a bundle).
• In process with CliRunner and the real bugfix bundle: a repeated bundle init keeps a local edit to the installed workflow (bytes compared, CRLF included) and leaves the registry alone; a plain bundle install does the same, and bundle install --refresh still restores the bundled file.
• bundle init with a changed bundle version exits 1 asking for --refresh, and leaves the bundle records and the edited workflow untouched.

With only src/ reverted to main, 3 of the 7 tests in the file fail (the delegation check, the repeated-init case and the changed-version case). With the fix, all 54 tests in test_command_init.py, test_command_install.py and test_commands.py pass.

Full suite on Linux, Python 3.13: 12093 passed, 374 skipped (uv sync --extra test, then pytest in that venv, 20m).

Ruff 0.15.0 (ruff check src tests) passes.

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (fill in the disclosure below)

AI disclosure: Two agents, both autonomous, working back and forth. Codex CLI (model: gpt-6-astra, reasoning effort max, autonomous, sandboxed and offline) found this while scouting the bundle commands, wrote the reproduction, and generated the fix, tests and docs paragraph. Claude Code (model: claude-opus-5-5, autonomous) reviewed the change, reran the tests against main and the fix, reran the repro with the real specify CLI, ran the full suite and lint, and drafted this description. Commits carry Assisted-by: trailers.

[Copilot]

🟢 Approval recommended

The focused fix has targeted regression coverage, with only a non-blocking documentation clarification remaining.

1 open finding

• Clarify repeated init behavior when bundle metadata changes · New

What changed in this PR

Prevents repeated Specify CLI bundle initialization from unintentionally refreshing installed components and overwriting local edits.

Changes:

• Passes refresh=False explicitly during bundle initialization.
• Adds regression coverage for preserved edits, changed-version rejection, and explicit refresh.
• Documents repeat-init behavior and refresh alternatives.

Tests were not rerun; regression results were assessed from the supplied evidence.

File	Description
tests/​specify_cli/​bundles/​test_command_init.py	Tests delegation, preservation, refresh, and version rejection.
src/​specify_cli/​bundles/​command_init.py	Explicitly disables implicit refresh.
docs/​reference/​bundles.md	Explains preservation and refresh options.

🧠 Review effort: Max

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[mnriem]

Please address Copilot feedback

[kartsan03]

Addressed Copilot's docs finding in 335d29f. The bundle init section now says a repeated init doesn't apply manifest changes: as with a plain bundle install, it fails without changing the installed bundle when the manifest changes the recorded bundle version, changes an owned component's version, source, preset priority or strategy, or removes an owned component. It points to bundle update and bundle install --refresh for those. This is the record check in installer.py that bundle init now goes through. Docs only; markdownlint passes on the file.

Drafted on behalf of @kartsan03 by Claude Code (model: claude-opus-5-5, autonomous), which also made the docs change.

[Copilot]

🟢 Approval recommended

The focused fix has targeted regression coverage, with only a nonblocking documentation correction remaining.

1 open finding

• Clarify bundle init behavior for additions versus manifest changes · New

1 resolved since last review

• Clarify repeated init behavior when bundle metadata changes

🧠 Review effort: Max

[mnriem]

Please address Copilot feedback. If not applicable, please explain why

[kartsan03]

Addressed Copilot's second docs finding in 2ceec75. The bundle init paragraph no longer says a repeated init doesn't apply manifest changes. It now says a repeated init follows the same rules as a normal bundle install: components newly added to the manifest are installed and recorded, while a changed bundle version or a changed or removed owned component still fails until bundle update or bundle install --refresh applies it. That matches the Install section and test_install_allows_reordered_components_and_additions. Docs only; markdownlint passes on the file.

Drafted on behalf of @kartsan03 by Claude Code (model: claude-opus-5-5, autonomous), which also made the docs change.

[Copilot]

🟢 Approval recommended

The focused fix has appropriate regression coverage and no identified blocking issues.

No open issues 🎉

1 resolved since last review

• Clarify bundle init behavior for additions versus manifest changes

_{Review effort: Max}