[Bug] init always writes project-local .mcp.json / .vscode/mcp.json, even with --no-editor-setup

[alex-systellar]

Describe the Bug

repowise init always merges a repowise entry into the repo-root .mcp.json and writes .vscode/mcp.json, with no way to opt out. --index-only, all --no-* flags, REPOWISE_SKIP_EDITOR_SETUP=1, and even the new --no-editor-setup (#1086) don't stop it — that flag only gates the machine-wide register_editor_clients path, while write_editor_project_files() still runs unconditionally in init_cmd/command.py.

This breaks running init as an automated setup step (e.g. on git worktree creation): every run leaves a dirty working tree, and repos that commit a hand-maintained .mcp.json get an unwanted diff each time.

Steps to Reproduce

1. In a clean repo, export REPOWISE_SKIP_EDITOR_SETUP=1
2. Run repowise init --index-only --no-workspace --no-claude-md --no-agents --no-codex --no-distill-hook --yes
3. Run git status

Expected Behavior

With --index-only plus the opt-out flags/env, init writes only .repowise/ and leaves the working tree untouched.

Actual Behavior

Repo-root .mcp.json is modified (a repowise entry merged into mcpServers) and .vscode/mcp.json is created. Nothing prevents it.

Environment

• OS: macOS 26.4 (25E246)
• Python version: 3.12.13
• Repowise version: 0.36.0
• Installation method: pip (--user)

Additional Context

I think with worktrees it's important to have a clean non-interactive init flag for setup bash scripts to init repowise

[RaghavChamadiya]

Confirmed, and your read of the cause is exactly right. Here is the full picture for whoever picks this up.

Why --no-editor-setup doesn't help. In init_cmd/command.py the two calls sit next to each other but only the second one is gated:

write_editor_project_files(console, repo_path, options=editor_options)   # command.py:1443
register_editor_clients(console, repo_path, no_editor_setup=not editor_setup)  # command.py:1448

is_editor_setup_disabled() (which is what reads both --no-editor-setup and REPOWISE_SKIP_EDITOR_SETUP) is only consulted inside register_editor_clients (cli/editor_setup.py:265). write_editor_project_files never asks. Workspace mode has the same split at init_cmd/workspace.py:464 and :775. That was intentional in #1086, whose flag help text says "Project-local files are unaffected", so this is a separate gap rather than a regression in that PR.

Which writes escape, specifically:

1. Repo-root .mcp.json: ClaudeCodeSetup.write_project_files calls save_root_mcp_config(repo_path) before it checks the claude_md disable flag (cli/editor_integrations/claude.py:38-40). So --no-claude-md doesn't stop it either; it only suppresses .claude/CLAUDE.md.
2. .vscode/mcp.json and .vscode/extensions.json: written by VSCodeSetup.write_project_files. Its vscode_mcp project-file id can only be disabled by the interactive prompt (prompt_for_project_files), and get_default_disabled_project_files() maps no CLI flag onto it. With --yes there is no way to decline.
3. .repowise/mcp.json also gets written, but that one lives under .repowise/ and is expected.

One more thing the repro doesn't cover: repowise update calls refresh_editor_project_files, and VSCodeSetup.refresh_project_files rewrites the same .vscode files. So even after a fix to init, the dirty tree would come back on the next update unless that path is gated too. (update does not rewrite root .mcp.json.)

Shape of a fix. The cleanest version I can see, without overloading the existing flag:

• Give root .mcp.json its own project-file id (say root_mcp) instead of writing it unconditionally inside the Claude integration, so it becomes gateable like claude_md and agents_md.
• Add a non-interactive way to disable the project-local set as a whole. Naming is open; a contributor should propose it in the PR. Honoring REPOWISE_SKIP_EDITOR_SETUP for project files too is tempting, but it would change behavior for existing CI users who currently rely on getting the in-repo files, so a new switch is probably safer.
• Gate refresh_editor_project_files on the same decision so update stays quiet as well.
• Tests belong in tests/unit/cli/test_editor_setup.py; assert that a gated run leaves nothing outside .repowise/.

Whether the persisted editor_files config should remember the opt-out (like --no-claude-md does) or stay per-run is a maintainer call worth settling in the PR.

Marking this help wanted. If you or anyone else wants to take it, say so here and I'll assign it.

[alex-systellar]

• Add a non-interactive way to disable the project-local set as a whole. Naming is open; a contributor should propose it in the PR. Honoring REPOWISE_SKIP_EDITOR_SETUP for project files too is tempting, but it would change behavior for existing CI users who currently rely on getting the in-repo files, so a new switch is probably safer.

this should be a completely new flag intended for autonomous setup

[rohitsalla]

/claim