[Problem] install-state keeps operations the current plan no longer contains, so doctor reports them missing forever

[philippschaedle]

What is the impact?

Doctor or repair does not recover the install

What happened?

I expected install-state to list only what the current install plan writes. Instead, it keeps operations from a previous install-state that the current plan no longer contains.

With install.sh --profile custom --enable-hooks --target claude --dry-run --json at 1ac07903, the plan has 955 plannedOperations, but statePreview.operations has 957. The two extra records are:

• copy-file hooks/hooks.json -> ~/.claude/hooks/hooks.json (no longer shipped for this target; hooks are registered in settings.json instead)
• copy-file scripts/lib/cost-estimate.js -> ~/.claude/scripts/lib/cost-estimate.js (source removed in 08c1c407)

Because the records survive every install, doctor.js reports them for good. The stale hooks.json copy shows as drifted, or as missing once it's removed, and cost-estimate.js always shows as a missing source. Neither a normal install nor uninstall plus install clears them. Uninstall keeps the drifted hooks.json copy, so the old install-state is not removed and gets carried into the next one.

Steps:

1. Install at a pin that ships hooks/hooks.json and scripts/lib/cost-estimate.js.
2. Update to 1ac07903 and install again.
3. Run node scripts/doctor.js --json: missing-source-files for cost-estimate.js, and drifted-managed-files for hooks.json.
4. Run uninstall, then install: both findings are still there.

Expected: records not in the current plan are dropped from install-state (and their files removed if unmodified, or reported once as orphaned).

Harness

Claude Code

Install method

Harness-specific installer target

Operating system

macOS

ECC and harness versions

ECC 2.2.1 at 1ac07903

Optional redacted diagnostics

claude-home: 1 managed file(s) are missing (~/.claude/hooks/hooks.json)
claude-home: 1 source file(s) referenced by install-state are missing (scripts/lib/cost-estimate.js)