writ has no command to refresh a repository it cloned; a layer's manifests stay at the clone's checkout until the user runs git by hand #812

Feature: #463 — writ command surface: layers, segments, adoption. Thread 3. Found on the Windows test, 2026-09-04.
Scheduling (USER, 2026-09-04): super high priority — addressed as soon as thread 2 (resource management) completes, ahead of the rest of thread 3.

writ repo add <layer> <url> clones the repository under the data home (devlore/writ/repos/<layer>) and writ
reads the layer's tree from that clone. Nothing in writ moves the clone forward afterwards: writ deploy and
writ upgrade read whatever the checkout holds, and upgrade regenerates copied files, not repositories.

Observed: #805 fixed the team layer's five packages-manifest.yaml files on develop, and writ deploy noblefactor
on the Windows machine kept failing on the old ones, because the clone still sat at the checkout repo add made.
The only remedy today is:

git -C %USERPROFILE%\.local\share\devlore\writ\repos\team pull

A user of writ should not have to know where the clone is, or that it is a clone.

Acceptance

• a writ command refreshes a cloned layer repository to its remote's current commit (name per the set/unset
  ruling and the writ repo set and unset replace add and remove: a layer has one registration, and re-pointing it is set #791–writ names a cloned repository by its layer; it should name it the way git clone does #793 surface; writ repo set over an existing clone is one candidate)
• writ deploy and writ upgrade state, in their narration, the commit each layer was read at
• a functional test: register a layer from a repository, advance the remote, refresh, and the deploy sees the
  new tree

Related

• pkg.Resource rejects the canonical purl form its doc promises: "pkg:winget/Vim/Vim?scope=machine" fails as unknown package manager "pkg" #813: the pkg purl-form refusal found on the same test, once the clone was refreshed by hand.
• packages-manifest.yaml files collide like deployed files: the most specific one shadows the rest, so a layer's general packages are never planned #814: manifests colliding like files, found on the same test.