* fix(refresh-marketplace): also enable stack plugins in workspace settings
Reconcile previously stopped at `claude plugin install --scope project`,
which only writes the global plugin registry. Without an entry in the
workspace `.claude/settings.json` `enabledPlugins` map, Claude Code
treats every plugin as disabled — `/plugins` doesn't list them and
their slash commands, skills, and agents are unreachable.
Refresh now writes the enable map after install/update, treating the
user's marketplace stack as the source of truth (re-enables anything a
prior `claude plugin disable` locally turned off). Override workspaces
are skipped via `is_override_workspace`.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* fix(override): sentinel governs init only, not runtime CLI
Sentinel `.claude/init-complete` with `override: true` was meant to
let admins ship INITIAL workspace content. The implementation was
over-scoped — `is_override_workspace` check sat inside every Agnes
writer (`install_claude_hooks`, `install_claude_commands`,
`maybe_refresh_claude_hooks`, `_enable_plugins_in_workspace_settings`),
which blocked runtime commands too. Operators on override workspaces
got trapped at the template snapshot: no `enabledPlugins` map from
`agnes refresh-marketplace`, no hook auto-migration from
`agnes self-upgrade`.
Move the check to the init-time call site (cli/commands/init.py,
`if not override_active:`) — the single place where init-time skip
is the right behavior. Writers themselves become unconditional;
runtime CLI now updates `.claude/` regardless of the sentinel.
Admin custom hooks survive — refresh only rewrites entries matching
`_OUR_COMMAND_MARKERS` (foreign commands fall through unchanged,
same contract as default workspaces).
Existing override workspaces auto-converge on next
`agnes self-upgrade` (fires from every SessionStart). No manual
migration.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Minas Arustamyan <arustamyan.minas@gmail.com>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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