fix(cli): reconcile cannot prune stale entries without a prior lock file

[pentaxis93]

Problem

reconcile_manifest_to_doc only prunes dependency entries that were previously tracked in the lock file (.groundwork/installed.lock.toml). On a fresh init — or after a failed init that never wrote a lock file — stale entries from an earlier run persist in agents.toml indefinitely.

Observed behavior

1. Ran groundwork init with a stale binary → wrote agents.toml with next_issue (stale) + other old entries
2. sk sync failed (because skills/next-issue doesn't exist on GitHub) → no lock file written
3. Rebuilt binary from current source, ran groundwork init again
4. Reconcile added the correct begin entry but left the stale next_issue entry in place
5. sk sync failed again — still trying to fetch the stale skills/next-issue path

Manual removal of the stale entry was required.

Root cause

read_previous_managed_aliases (main.rs:945) returns an empty set when no lock file exists. prune_stale_managed_dependencies (main.rs:956) only prunes entries where previously_managed.contains(k) && !desired_aliases.contains(k). With an empty previously_managed set, nothing qualifies for pruning — even entries pointing to pentaxis93/groundwork paths that are clearly managed by groundwork.

Structural gap

The pruning heuristic assumes that if an entry isn't in the lock file, it's user-owned and should not be touched. This is safe in the general case but breaks when a stale binary writes groundwork-managed entries that never make it into a lock file.

A possible distinguishing signal: entries with gh = "pentaxis93/groundwork" whose path matches skills/* are groundwork-managed by definition, regardless of lock file state. The reconcile could use repo + path pattern as an additional ownership signal.

Relevant code

• main.rs:945-954 — read_previous_managed_aliases (empty set when no lock file)
• main.rs:956-975 — prune_stale_managed_dependencies (only prunes previously-managed entries)
• main.rs:903-942 — reconcile_manifest_to_doc (orchestrates prune + upsert)

Acceptance criteria

• groundwork init cleans up stale groundwork-managed entries even without a prior lock file
• External (non-groundwork) dependencies are never pruned without lock file evidence

[pentaxis93]

Implemented and merged in PR #114 (commit 1706404). Closing as complete.