docs: explain .squad/templates/ runtime inputs vs generated/stale copies (source template) #1494

Split off from #1436.

Problem

.squad/templates/ mixes two very different kinds of files, and there is nothing in the repo (or in the generated project) that tells you which is which:

• Runtime inputs that the coordinator, squad copilot, squad rc, and agent bootstrap read on every run. Deleting these breaks generated projects immediately.
• Generated / stale copies produced once by squad init and never read back (concretely: .squad/templates/workflows/ and .squad/templates/skills/ as verified in the enhancement: drop template folder from .squad #1436 investigation). These are just duplicates of what the CLI already ships.

New contributors and users who look at the folder cannot tell the safe-to-prune subtrees from the load-bearing ones. This has already caused confusion (#1436).

What to do

Add a source-of-truth reference that ships with the CLI and lands in generated projects, most likely a .squad/templates/README.md template that is itself part of squad init output. It should:

1. List every subtree under .squad/templates/ and label each one as runtime input or stale copy from init.
2. For runtime inputs, name the code path that reads it (e.g. "read by packages/squad-sdk/src/... during agent spawn") so future refactors update the doc.
3. Call out the two subtrees that are safe to remove today (workflows/, skills/) once enhancement: drop template folder from .squad #1436 lands, and link to enhancement: drop template folder from .squad #1436.
4. State the invariant: nothing under .squad/templates/ should be added without also being registered as either a runtime input (with a code reference) or an intentionally-generated file (with an init reference).

Nice to have

• A squad doctor check that flags files under .squad/templates/ in the generated project that are neither a documented runtime input nor a currently-generated file, so drift is caught early.

Related

• Tracker: enhancement: drop template folder from .squad #1436
• Companion follow-up: workflow local-edit preservation split from enhancement: drop template folder from .squad #1436