Gregory Schier 8bd26d0f24 Consult the manifest before deleting skill files ...

Two problems found in review, both from deleting without checking what we
actually wrote:

`agent remove` called remove_dir_all on the whole tree, discarding files
the user had edited or added. Install goes out of its way to preserve
those, so uninstall throwing them away was inconsistent and lossy. It now
deletes only tracked files whose contents still match the manifest,
prunes empty directories, and reports anything it kept.

`agent install` never reconciled against the previous manifest, so a file
an older CLI shipped but a newer one drops would linger and could feed an
agent stale guidance. Unshipped files are now removed when unmodified,
and left alone (and untracked) when the user has edited them.

2026-08-13 21:24:16 -07:00

..

yaak-cli

Consult the manifest before deleting skill files

2026-08-13 21:24:16 -07:00