docs(skills): upstream syncs run in their own worktree

[yordis]

• A sync installs dependencies, rewrites the lockfile, and runs the full suite, which disrupted the main checkout that often serves the live T3 Code session and holds uncommitted work.
• The last sync had to stash local changes to get a clean tree, and its install rewrote a generated file in the main checkout.

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[cursor]

PR Summary

Low Risk
Documentation-only change to the upstream sync agent skill; no runtime or application code is modified.

Overview
Updates the trogonstack-sync-upstream agent skill so upstream merges never run in the main checkout.

Prepare now requires fetching origin and upstream without stashing or switching branches, uses origin/main..upstream/main to detect whether a sync is needed, and lists fork-only commits against origin/main.

Create the sync branch documents a sibling git worktree, scripts/setup-worktree.ts (with T3CODE_PROJECT_ROOT from the primary worktree), then git merge upstream/main. Branch numbering also checks git worktree list; all later steps—including re-running vp i after lockfile conflicts—run inside that worktree.

After merge, cleanup removes the worktree from the main checkout before deleting the sync branch.

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