graft init --dry-run ignores suppression flags and omits files changed by init #329

Summary

graft init --dry-run does not currently describe the operation that a real init would perform:

1. The plan ignores --no-global, --no-mcp, and --no-hooks for non-Claude hosts.
2. It omits other files that init can create, modify, or delete, including the wiring stamp, retraction targets, and graph-build side effects.

This makes --dry-run unsafe as a preflight check, especially because its help text says it will "print every file init would touch."

Environment

• @nanonets/graft 0.16.0
• macOS 26.6.2, arm64
• Node.js 24.17.0
• Also verified against current main at 3a85a2f40e283ac0c9b617d9a4bead18d73c3c70

Reproduction: suppression flags are not reflected

Run these in a repository where the agents host is available:

graft init --dry-run --agents agents --no-build
graft init --dry-run --agents agents --no-build --no-global --no-mcp --no-hooks

On 0.16.0, both commands print the same planned writes. The second command still reports:

would write — this repo:
  AGENTS.md      fenced graft section
  opencode.json  mcp.graft

would write — your machine, affects ALL repos:
  ~/.codex/config.toml                  [mcp_servers.graft]
  ~/.codex/hooks/graft/graft-hooks.cjs  post-edit hook shim
  ~/.codex/hooks.json                   SessionStart / UserPromptSubmit / PostToolUse / Stop

The real writer does apply these flags:

• runHostsInit() skips MCP writes when mcp === false.
• It skips global Codex hooks when hooks === false or global === false.
• MCP config writers receive the global option.

The dry-run path does not. On current main, src/cli.ts calls planInit(repo, { home }), while src/hosts/plan.ts adds MCP and hook targets unconditionally.

Reproduction: the plan is incomplete

Even after the flag mismatch is fixed, the plan does not include all paths a real run may touch:

• writeStamp() writes graft/.cache/wiring-stamp.json, including with --no-build.
• runRetract(..., { apply: true, exclude: ids }) can modify or delete wiring for previously selected hosts before the new wiring is written.
• When the graph is missing and --no-build is not used, buildGraphIfMissing() runs graft build, which creates the generated graft/ tree and may update .gitignore and .ignore.

The dry-run branch returns before these operations and does not report them.

Expected behavior

--dry-run should match the real operation for the same arguments:

• Omit targets disabled by --no-global, --no-mcp, and --no-hooks.
• Report files that would be modified or deleted by retraction.
• Report the wiring stamp and graph/build outputs when applicable, or explicitly label generated output directories/side effects if enumerating every generated file is impractical.

An alternative would be to narrow the command/help contract and clearly state that the output covers only agent wiring targets, but it should still apply the suppression flags accurately.

Suggested implementation direction

• Pass global, mcp, hooks, and build into the planning layer.
• Build non-Claude host plans through the same predicates used by runHostsInit().
• Reuse planRetract() with apply: false and the same exclude/global options to include removals.
• Add the wiring stamp and graph-build side effects to the plan.
• Add a flag-matrix test comparing the planned target set with an instrumented real writer.

Related work

#118 and draft PR #124 address the narrower issue where Claude Code itself ignores --no-mcp / --no-hooks. PR #124 makes Claude targets aware of those two flags, but its non-Claude HOSTS.map(...) plan still adds MCP/hooks unconditionally, does not model --no-global, and does not include retraction, stamp, or build side effects. This report is intended to track the remaining dry-run contract rather than duplicate #118.