fix: v0.45.1 — refuse multi-repo workspace parent (cross-project index bleed)

[Shahinyanm]

Problem

When a Claude Code session is launched from a non-git workspace parent that nests several project repos — e.g. /home/.../loom holding token-pilot, loom-host, aimux, task-jorunal — token-pilot indexed all of them into one ast-index. Symbol lookups then bled across projects: find_usages / read_symbol returned matches from the wrong repo, or symbol not found.

Root cause

start.sh always passes an explicit root:

PROJECT_ROOT="${CLAUDE_PROJECT_DIR:-$USER_CWD}"
exec node "$SCRIPT_DIR/dist/index.js" "$PROJECT_ROOT"

So in startServer explicitRoot is always truthy → the entire git-root narrowing block (if (!explicitRoot)) is skipped and the raw arg is used verbatim. When that arg is a workspace parent (not a git repo), isDangerousRoot doesn't catch it (it only guards system/home dirs), so ast-index scans every sibling repo.

Fix

New guard isMultiRepoParent(root) in core/validation.ts: returns true for a non-git directory with >=2 immediate child git repos. On match:

• skipAstIndex is set (ast-index disabled) — fail safe instead of bleeding.
• A warning tells the user to set CLAUDE_PROJECT_DIR to the specific project.

Wired into:

• startServer (src/index.ts) — skipAstIndex + warning.
• server.ts MCP-roots auto-detect (Strategy 1) — a client-reported parent is rejected too. Strategy 2 (git toplevel) is inherently single-repo, left untouched.

Unaffected: single-repo roots, monorepos, and roots that are themselves a git repo (submodules/vendored repos underneath stay intentional).

Tests

tests/core/multi-repo-parent.test.ts — 7 cases: >=2 child repos -> true; one/zero child repos -> false; root is itself a repo -> false; .git-as-file (submodule/worktree) counted; missing path / empty string -> false. tsc --noEmit clean.

Note: 3 pre-existing context-mode-detector test failures and full-suite parallel flakiness exist on master independently of this change (sequential run is clean aside from those 3).

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