Main flow bugs: init, sync, hooks and plugin commands #413

What and why

Bugs in the commands every user runs: init, sync, hook dispatch, and use, status and search. Each PR fixes one area, and they are meant to ship together in v0.6.0.

Zulip discussion

No response

RFD

No response

Code PRs

• fix: issues found by end-to-end testing #366
• fix(hooks): keep a failing plugin hook's output and time out hooks that hang #388
• fix(config): harden init and startup against unknown agents, unwritable logs and empty env vars #389
• fix: match plugin names consistently in status, use and search #390
• fix(sync): install skills atomically and serialize concurrent syncs #391
• fix(pm): serve chained crates from the cargo cache outside sync, and fix two workspace lookups #392