bug(runtime): linked worktree boundaries omit the Git commondir

## What happened

In a linked Git worktree opened with macOS sandbox mode set to Auto, approving the requested `.git/worktrees/` subtree leaves the repository's shared Git metadata inaccessible. After individual shared files such as `config` and `packed-refs` are approved, `git status --short --branch` can exit `0`, warn that `.git/info/exclude` is inaccessible, and list tracked files as additions. `git log` can report that the current branch is broken.

## How to reproduce

1. Create a linked worktree from a repository with tracked files:

```sh
MAIN="$HOME/path/to/main-checkout"
WORKSPACE="$HOME/path/to/linked-worktree"
git -C "$MAIN" worktree add -b boundary-repro "$WORKSPACE"
```

2. Open `$WORKSPACE` in Maka on macOS.
3. Keep sandbox mode set to Auto with the workspace-write profile.
4. Run `git status --short --branch` through the managed Bash tool.
5. Approve the boundary request for `$MAIN/.git/worktrees/` and the individual shared Git metadata files requested afterward.

The command can return `0` with an inaccessible `.git/info/exclude` warning and a false list of added files.

## Expected

A read-scoped subtree request for a standard linked-worktree admin directory should be normalized to the repository's shared `.git` directory before approval. One read approval should let `git status` and `git log` read the real refs, objects, configuration, and excludes. Write operations such as `git commit` should keep their exact requested path and require separate approval.

## Root cause

`packages/runtime/src/sandbox-boundary-path.ts:80-108` canonicalizes paths and scopes while omitting the linked-worktree `commondir` relationship. `packages/runtime/src/builtin-tools.ts:743-749` supplies only the current working directory as the workspace root, so the main checkout's shared `.git` directory remains outside the managed boundary.

## Environment

- Maka commit: `4cbe224`
- OS: macOS 26.6.1
- Surface: Runtime managed Bash / Auto sandbox
- Node.js: 24.19.0

Start with packages/runtime/src/sandbox-boundary-path.ts:80-108 and packages/runtime/src/builtin-tools.ts:743-749, then reproduce the linked-worktree case with git status --short --branch and git log through the managed Bash tool. Trace how the commondir relationship and workspace root are handled. Done means read-scoped approvals reach the shared .git directory while writes retain their exact requested paths and require separate approval.

Written by the indexing model from the issue text.