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.