fix: address PR 68 review findings (doctor UX)

AGENTS.md

@@ -54,7 +54,7 @@ src/
     registry.rs        — Registry management subcommands
     activate.rs        — Plugin + module activation (Phase 3 & 4); public entry: execute_with_candidate_runner
     init.rs            — `numan init [--refresh]`: Nu probe, paths cache, auto-configures official registry
-    doctor.rs          — `numan doctor [--scan]`: health checks + safe repairs by default (or report-only with `--scan`) (Phase 7.2; spec: docs/numan-doctor.md)
+    doctor.rs          — `numan doctor [--scan] [--json]`: repairs by default; `--scan` report-only (Phase 7.2; spec: docs/numan-doctor.md)
     snapshot.rs        — `numan snapshot list|inspect|delete|rollback` (Phase 5.3)
     deactivate.rs      — Plugin + module deactivation: journaled plugin unregister (`execute_with_unregistrar`); module full/partial (Phase 4 / Issue #22 PR2)
     plugin_lifecycle.rs — Activate/deactivate-owned lifecycle boundary exposed to opt-in update orchestration (Issue #22 PR3)
@@ -109,8 +109,7 @@ tests/
   fixtures/nupm/       — supported/rejected fixture corpus for parser/classifier tests
   init_test.rs          — `numan init` / `init --refresh` (vendor drift, managed-file revalidation)
   completions_test.rs  — shell completion script generation (Phase 7.3)
-  doctor_test.rs       — `numan doctor` report-only (`--scan`), default auto/confirm tiers, journal checks (Phase 7.2)
-  nupm_compat_test.rs  — Phase 6 integration tests (T13–T25, import/drift/manifest/activation/platform)
+  doctor_test.rs       — `numan doctor` default repairs, `--scan` report-only, journal checks (Phase 7.2)  nupm_compat_test.rs  — Phase 6 integration tests (T13–T25, import/drift/manifest/activation/platform)
   nupm_real_nu_test.rs — Phase 6.4 real-Nu #[ignore] acceptance tests (run with `cargo test -- --ignored`)
   plugin_lifecycle_real_nu.rs — Issue #22 smoke marker (points at Stage 1 + active-update suite)
   plugin_active_update_real_nu.rs — Issue #22 active-update real-Nu matrix (fixture dual-version registry; Nu 0.113.x; skipped on default PR ignored job)
@@ -152,7 +151,7 @@ tests/
 4. **Lockfile pins immutable paths** — cached artifacts retained while referenced
 5. **Registry trust** — Ed25519 signatures over exact `index.json` bytes; bypass requires `NUMAN_ALLOW_UNSIGNED=1` (dev only)
 6. **Artifact SHA256 is mandatory for plugins** — the install transaction bails if `sha256` is missing from a binary artifact
-7. **State snapshots before mutation** — `create_snapshot()` before `install`/`update`/`remove`/`activate`/`deactivate`/nupm-import mutations; `numan gc` treats every snapshot's referenced payloads as live roots
+7. **State snapshots before mutation** — `create_snapshot()` before `install`/`update`/`remove`/`activate`/`deactivate`/`init --refresh`/nupm-import/doctor repair mutations; `numan gc` treats every snapshot's referenced payloads as live roots
 8. **Platform triple** — comes from `#[cfg(target_env)]` at compile time, not `std::env::consts` (see `core/platform.rs`; `LIBC` is a compile-time const)
 
 ## Development Workflow

Cargo.toml

@@ -83,5 +83,4 @@ libc = "0.2"
 [dev-dependencies]
 tempfile = "3"
 rand_core = { version = "0.6", features = ["getrandom"] }
-libc = "0.2"
 wait-timeout = "0.2"

README.md

@@ -44,7 +44,7 @@ Numan is **early-stage**. Core install, activate, update, remove, gc, registry,
 - **Module autoloads** — managed vendor autoload files with ownership markers and candidate validation
 - **Lifecycle management** — `update`, `remove`, and `gc` with pending-lifecycle journal recovery
 - **nupm interoperability** — `numan nupm status|inspect|import|diff` for migration from [nupm](https://github.com/nushell/nupm)
-- **Health checks** — `numan doctor [--fix]` diagnoses root state and applies safe repairs
+- **Health checks** — `numan doctor` diagnoses root health and applies safe repairs by default; `--scan` reports only
 - **Shell completions** — bash, fish, zsh, PowerShell, and Nushell via `numan completions`
 
 ---
@@ -187,7 +187,7 @@ Or pick a package yourself (`numan search` hides incompatible hits by default; u
 numan search nutest
 numan info vyadh/nutest
 numan install vyadh/nutest
-numan activate vyadh/nutest --yes
+numan activate vyadh/nutest
 ```
 
 Install is **inert** — nothing is registered with Nu until you run `numan activate` (or `numan try`, which activates after install). If a package needs a different Nu minor, Numan explains the mismatch and can offer `numan setup nu <x.y.z>` (activations are per-Nu; re-activate after switching). When no compatible starter exists, `numan try` suggests installing a matching managed Nu version or searching for another package with `numan search`.
@@ -352,7 +352,7 @@ Global flag: `--root <path>` — override the Numan root directory (all commands
 | `nupm status` | `--nupm-home <path>` |
 | `nupm inspect` | `--all` scan home; `--nupm-home <path>`; `--exit-on-ineligible` fail on ineligible |
 | `nupm import` | `--as owner/name` (single import); `--manifest <file>` (batch); `--nupm-home <path>`; `--yes` skip consent |
-| `doctor` | `--scan` report-only; `--json` machine output; `--nupm-home <path>` |
+| `doctor` | `--scan` report only; `--json` machine output; `--nupm-home <path>` (repairs by default) |
 | `setup nu` | `--force` re-download; `--skip-path` don't update PATH; `--yes` skip prompt |
 
 Run `numan <command> --help` for full flag documentation.
@@ -432,7 +432,7 @@ For the cross-repository plan snapshot (as of 2026-07-29) across `numan`,
 | **5** | `update` / `remove` / `gc`, lockfile v2, [snapshots + rollback](docs/snapshots-and-rollback.md) | ✅ (source builds deferred) |
 | **6** | [nupm](docs/nupm-compatibility.md) status, inspect, import, drift | ✅ |
 | **7** | Doctor, completions, onboarding, CI hardening, [winget packaging](docs/PACKAGING.md) | ✅ — [plan](docs/plans/Phase7Plan.md) |
-| **Post-7.6** | Production [official registry](https://tonythethompson.github.io/numan-registry/) cutover; `numan init` and `numan doctor --fix` auto-configure `official` | ✅ (v0.1.4) |
+| **Post-7.6** | Production [official registry](https://tonythethompson.github.io/numan-registry/) cutover; `numan init` and `numan doctor` auto-configure `official` | ✅ (v0.1.4) |
 
 ### Next (toward 1.0)