Two related fixes surfaced from a real sf headless auto run in dr-repo.
1. Project preferences now resolve from the MAIN worktree, not the
current linked worktree. SF's auto-mode creates a git worktree per
milestone (`.sf/worktrees/M003/`). The old code called
`projectPreferencesPath()` which used `process.cwd()` — the
milestone worktree — so a pref change on main (service_tier,
dynamic_routing, model config) never reached an in-flight milestone
until the branch merged main. Observed concretely when disabling
dynamic_routing had no effect until we merged main into the
milestone branch.
New `projectPrefsRoot()` detects a linked worktree by reading
`.git` (a FILE in worktrees, pointing to
`/main/.git/worktrees/NAME`), follows the `commondir` pointer back
to the main `.git` dir, and walks up one level. Falls back to cwd
silently for non-worktree setups.
2. MCP server config now also loads from global paths
(`~/.sf/mcp.json`, `~/.sf/agent/mcp.json`) in addition to the
existing project-level (`.mcp.json`, `.sf/mcp.json`). First-hit
wins, so project configs can still shadow or augment a globally-
registered server by name. This lets the user register unauth'd
servers like the DeepWiki remote MCP once and have every SF
project pick it up without per-project `.mcp.json`.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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