refactor: UX improvements — reduce prompts and simplify doctor

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 [--fix] [--yes]`: health checks + safe repairs (Phase 7.2; spec: docs/numan-doctor.md)
+    doctor.rs          — `numan doctor [--scan]`: health checks + safe repairs by default (or report-only with `--scan`) (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)
@@ -64,7 +64,7 @@ src/
     nupm.rs            — `numan nupm status|inspect|import|diff`: nupm discovery + import + drift (Phase 6.1–6.3)
     completions.rs     — `numan completions <shell>`: bash/fish/zsh/powershell/nushell scripts (Phase 7.3)
     setup.rs           — `numan setup nu [VERSION]|remove|path|use <path>` + `setup loader`: Nushell bootstrap + nushell-loader install
-    try_cmd.rs         — `numan try [--yes] [--no-activate]`: curated starter install + activate for current Nu
+    try_cmd.rs         — `numan try [--no-activate]`: curated starter install + activate for current Nu
     use_cmd.rs         — `numan use <version>|latest|list`: activates a previously installed managed Nu version (no auto-download); writes the active-version marker after a PreMutation snapshot under the root mutation lock
     nu_pin_offer.rs    — Shared TTY offer to `setup nu <version>` + `init --refresh` on Nu mismatch
   install/
@@ -109,7 +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, --fix auto tier, journal checks (Phase 7.2)
+  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)
   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)
@@ -152,7 +152,7 @@ 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

@@ -76,6 +76,10 @@ uuid = { version = "1", features = ["v7", "v4"] }
 # Git (for source builds and registry sync)
 git2 = "0.21"
 
+# stdio redirect for doctor --json repair passes (Unix only)
+[target.'cfg(unix)'.dependencies]
+libc = "0.2"
+
 [dev-dependencies]
 tempfile = "3"
 rand_core = { version = "0.6", features = ["getrandom"] }

README.md

@@ -269,8 +269,8 @@ See [docs/snapshots-and-rollback.md](docs/snapshots-and-rollback.md) for scope,
 #### 6. Verify health
 
 ```bash
-numan doctor                      # report-only diagnosis
-numan doctor --fix --yes          # apply safe automated repairs
+numan doctor                      # diagnose and apply safe automated repairs
+numan doctor --scan               # report-only diagnosis
 ```
 
 ---
@@ -308,7 +308,7 @@ Global flag: `--root <path>` — override the Numan root directory (all commands
 | Command | Description |
 |---------|-------------|
 | `numan init [--refresh]` | Probe Nu and cache paths for activation |
-| `numan try [--yes] [--no-activate]` | Install and activate a curated starter package for your Nu + platform (prefers Nu 0.114 starters; suggests managed Nu pin or search if no compatible starter) |
+| `numan try [--no-activate]` | Install and activate a curated starter package for your Nu + platform (prefers Nu 0.114 starters; suggests managed Nu pin or search if no compatible starter) |
 | `numan search <query>` | Search registry by name, description, or tags |
 | `numan info <owner/name>` | Show package metadata and available versions |
 | `numan install <owner/name[@version]>` | Download, verify, extract, and lock |
@@ -336,23 +336,23 @@ Global flag: `--root <path>` — override the Numan root directory (all commands
 | `numan nupm import --manifest file.toml` | Batch import from manifest |
 | `numan nupm diff <owner/name>` | Compare imported payload vs nupm source |
 | `numan completions <shell>` | Generate bash, fish, zsh, powershell, or nushell completions |
-| `numan doctor [--fix] [--yes] [--json]` | Diagnose root health; optional safe repairs |
+| `numan doctor [--scan] [--json]` | Diagnose root health and repair (use `--scan` for report-only) |
 
 ### Common flags (by command)
 
 | Command | Flags |
 |---------|-------|
 | `install` | `--force` reinstall; `-v` / `--verbose` |
-| `activate` | `--yes` skip prompt; `--verbose`; `--list` status only; `--check` integrity only |
-| `deactivate` | `--yes` skip prompt; `--verbose` |
+| `activate` | `--verbose`; `--list` status only; `--check` integrity only |
+| `deactivate` | `--verbose` |
 | `update` | `--check` report only; `-v` / `--verbose` |
 | `remove` | `--force` remove despite active activation |
 | `gc` | `--dry-run` preview only |
 | `registry add` | `--key <base64-public-key>` (required for custom registries; official is auto-configured on `init`) |
 | `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` | `--fix` apply safe repairs; `--yes` skip confirm tier; `--json` machine output; `--nupm-home <path>` |
+| `doctor` | `--scan` report-only; `--json` machine output; `--nupm-home <path>` |
 | `setup nu` | `--force` re-download; `--skip-path` don't update PATH; `--yes` skip prompt |
 
 Run `numan <command> --help` for full flag documentation.