Fix doctor managed Nu reporting and improve registry packages listing

AGENTS.md

@@ -66,7 +66,8 @@ src/
     completions.rs     — `numan completions <shell>`: install by default (mkdir+write); `--print` for stdout (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
-    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
+    use_cmd.rs         — `numan use <version>|latest|list`: activates a previously installed managed Nu version (no auto-download); cross-minor leave/teardown (modules then plugins) + restore (plugins then modules) via activation profiles; same-target is restore-only; writes the active-version marker after a PreMutation snapshot under the root mutation lock
+    activation_switch.rs — shared leave/restore orchestration for `numan use` (lower-level lifecycle, no profile-sync wrappers)
     nu_pin_offer.rs    — Shared TTY offer to `setup nu <version>` + `init --refresh` on Nu mismatch
   install/
     download.rs        — HTTP download with progress
@@ -84,6 +85,7 @@ src/
     migration_journal.rs — `state/migration-journal.json` for legacy-Nu single-binary → versioned-layout transition (Prepared → Renamed → Active stages); self-heal at top of `migrate_legacy_install_with_detector`, reconciled by `numan doctor --fix` (auto-tier repair)
     snapshot.rs        — Immutable activation snapshots (`create_snapshot`, `list_snapshots`, etc.)
     rollback.rs        — Journaled restore of Numan-owned state to a snapshot
+    activation_profile.rs — Desired per-Nu-minor activation sets (`nu_state/activation-profile.json`); leave union; user activate/deactivate/remove sync
     nupm_import.rs     — nupm-import provenance (`state/nupm-imports.json`, Phase 6.2)
   nu/
     bootstrap.rs        — download/install official Nushell release under tools/nushell
@@ -147,6 +149,7 @@ tests/
 - **Plugin deactivate journal**: `state/pending-plugin-deactivate.json` (`Prepared` → `Unregistered` → clear lockfile `activation`); reconciled on next `deactivate`; doctor warns `journal.plugin_deactivate_pending`
 - **Migration journal**: `state/migration-journal.json` for the legacy-Nu single-binary → versioned layout transition. Stages `Prepared` (before `create_dir_all`) → `Renamed` (after legitimate `rename`) → `Active` (after `write_active_version`); journal deleted on transition to `Active`. Every well-formed pending journal stage (`Prepared`, `Renamed`, and `Active`) is reconciled by `numan doctor --fix` (Auto-tier, fix hint `numan use`) and by the self-healing `reconcile(root)?` at the top of every `migrate_legacy_install_with_detector` call; file-system truth takes precedence over journal stage when they disagree. Unreadable or schema-mismatched journals emit `journal.migration_invalid` (Error severity, Manual repair tier: delete the stale journal); they are not auto-reconciled. `reconcile` refuses to act when `tools/nushell` is a symlink or reparse point (`assert_not_symlink` guard); the journal is left unchanged on that path so a follow-up attempt can succeed once the symlink is resolved. A `Prepared`-stage orphan directory that cannot be removed (e.g. ENOTEMPTY) causes `reconcile` to return `Err` and retain the journal so the next invocation can retry.
 - **Active version marker**: `nu_state/active-version.json` (`{ "version": "X.Y.Z" }`, optionally `{ "version": "X.Y.Z", "binary_path": "/abs/path/to/nu" }` for off-tree selections). Sole authority for which `tools/nushell/<v>/` is selected. Written by `numan setup nu` and `numan use <version>|latest`. The optional `binary_path` records the resolved off-tree binary when `numan setup nu use <path>` swaps to a user-supplied Nu so subsequent `numan use list` and `find_nu_executable_with_root` can resolve the chosen version even when no on-tree install exists (the field uses `#[serde(default, skip_serializing_if = "Option::is_none")]` so the on-disk shape stays `{ "version": ... }` for on-tree selections and pre-existing markers still load).
+- **Activation profile**: `nu_state/activation-profile.json` stores desired per-Nu-minor plugin/module sets. Cross-minor `numan use` unions currently Numan-active packages into the leaving minor (never shrinks), tears down modules then plugins, switches the marker, then restores the target minor (plugins then modules). Same-target `use` only reconciles missing desired activations. User `activate`/`deactivate` are idempotent desired-state ops on the current minor; `remove` deletes the id from all minors. `numan use` calls lifecycle beneath profile-sync wrappers so leave/restore do not wipe saved desire.
 - **Atomic writes**: all JSON state files (lockfile, journal, nu_state/paths.json) use `write_json_atomic` (tempfile in same dir + persist) — no partial-write corruption
 - **Function signatures**: use `&Path` not `&PathBuf` in function parameters (clippy::ptr_arg is CI-enforced)
 

CHANGELOG.md

@@ -11,10 +11,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - **Release assets** for `aarch64-unknown-linux-gnu` and `aarch64-pc-windows-msvc` (native ARM runners); `numan update --self` maps those triples
 - **Homebrew** Linux ARM archive support; **winget** verifies and submits both Windows x64 and ARM64 zips
+- **`numan use` activation profiles**: cross-minor switches auto-deactivate Numan-active plugins/modules (leave profile is a never-shrinking union per Nu minor in `nu_state/activation-profile.json`) and restore the target minor's desired set after the marker write. Same-target `use` is restore-only reconcile. User `activate`/`deactivate` keep the current minor's desired set in sync (idempotent even when already active/inactive); `remove` clears the package id from every minor.
 
 ### Changed
 
 - **`numan completions <shell>`** installs by default (creates the target directory if needed). Use `--print` to emit the script on stdout for piping or custom redirects.
+- **`numan registry packages`**: clearer listing (blank line between entries, styled id/version/type, soft-wrapped dim descriptions)
 
 ### Fixed
 
@@ -38,6 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
   Then open a new terminal and confirm with `$env:Path -split ';'`.
 
+- **`numan doctor`**: report versioned managed Nu installs (`tools/nushell/<version>/nu`) instead of only the legacy `tools/nushell/nu` path
 - **`numan setup nu`**: official Nushell 0.114.x release archives exceed the old
   256 MiB extract cap (~279 MiB uncompressed on linux-gnu). Bootstrap now
   extracts only the `nu` binary (skipping bundled plugins) and raises the

README.md

@@ -354,8 +354,8 @@ Global flag: `--root <path>` — override the numan root directory (all commands
 | `numan setup nu remove` | Remove the managed Nushell install and fall back to PATH Nu |
 | `numan setup nu path` | Use the Nushell already on PATH (removes managed install) |
 | `numan setup nu use <path>` | Register a specific existing Nushell binary |
-| `numan use <version>` | Switch the active managed Nu to a pinned version (no auto-install; errors with a hint to run `numan setup nu <version>` if missing) |
-| `numan use latest` | Switch the active managed Nu to the latest installed version |
+| `numan use <version>` | Switch the active managed Nu to a pinned version (no auto-install; errors with a hint to run `numan setup nu <version>` if missing). Cross-minor switches deactivate Numan-active plugins/modules for the leaving Nu and restore that minor's remembered set when you switch back. |
+| `numan use latest` | Switch the active managed Nu to the latest installed version (same leave/restore behavior as `use <version>`) |
 | `numan use list` | List installed managed Nu versions and mark the active one |
 | `numan nupm status` | Summarize nupm home and import eligibility |
 | `numan nupm inspect [--all] [path]` | Classify nupm packages at a path |

src/cmd/activate.rs

@@ -138,6 +138,8 @@ fn execute_with_registrar_and_runner(
     // These are already caught in resolve functions.
 
     if plugin_targets.is_empty() && module_targets.is_empty() {
+        // Already-active (or inactive-but-requested) packages still need profile sync.
+        sync_user_activate_profile(root, &nu_paths, args, &lockfile)?;
         println!("Nothing to activate.");
         return Ok(());
     }
@@ -177,6 +179,7 @@ fn execute_with_registrar_and_runner(
     let module_targets = resolve_module_targets(args, &lockfile, &nu_paths)?;
 
     if plugin_targets.is_empty() && module_targets.is_empty() {
+        sync_user_activate_profile(root, &nu_paths, args, &lockfile)?;
         println!("Nothing to activate.");
         return Ok(());
     }
@@ -238,6 +241,10 @@ fn execute_with_registrar_and_runner(
         }
     }
 
+    // Reload lockfile so profile sync sees post-activation state for "activate all".
+    let lockfile = Lockfile::load(root)?;
+    sync_user_activate_profile(root, &nu_paths, args, &lockfile)?;
+
     if any_failed {
         bail!(
             "One or more packages failed to activate. Successful activations have been persisted."
@@ -247,6 +254,28 @@ fn execute_with_registrar_and_runner(
     Ok(())
 }
 
+fn sync_user_activate_profile(
+    root: &Path,
+    nu_paths: &NuPaths,
+    args: &ActivateArgs,
+    lockfile: &Lockfile,
+) -> Result<()> {
+    let ids = if args.packages.is_empty() {
+        let active = crate::cmd::activation_switch::collect_currently_active(lockfile, nu_paths);
+        let mut all = active.plugins;
+        all.extend(active.modules);
+        all
+    } else {
+        args.packages.clone()
+    };
+    crate::cmd::activation_switch::sync_profile_after_user_activate(
+        root,
+        &nu_paths.nu_version,
+        &ids,
+        lockfile,
+    )
+}
+
 // ── Plugin lane ────────────────────────────────────────────────────────────────
 
 /// Run the plugin registration lane. Returns `true` if any plugin failed.
@@ -569,6 +598,45 @@ fn run_module_lane(
     Ok(false) // lane succeeded
 }
 
+/// Activate named modules without acquiring the mutation lock, snapshotting, or
+/// syncing the activation profile. Caller must hold the root mutation lock.
+///
+/// Returns `true` if the module lane reported failure.
+pub(crate) fn activate_modules_unlocked(
+    root: &Path,
+    package_ids: &[String],
+    runner: &dyn CandidateRunner,
+) -> Result<bool> {
+    if package_ids.is_empty() {
+        return Ok(false);
+    }
+
+    let nu_paths = NuPaths::load(root)?;
+    nu_paths.validate_drift()?;
+    let mut lockfile = Lockfile::load(root)?;
+
+    let args = ActivateArgs {
+        packages: package_ids.to_vec(),
+        verbose: false,
+        list: false,
+        check: false,
+    };
+    let module_targets = resolve_module_targets(&args, &lockfile, &nu_paths)?;
+    if module_targets.is_empty() {
+        return Ok(false);
+    }
+    let managed_file_path = resolve_managed_file_path(&nu_paths)?;
+    run_module_lane(
+        root,
+        &nu_paths,
+        &mut lockfile,
+        &module_targets,
+        &managed_file_path,
+        runner,
+        None,
+    )
+}
+
 // ── --list subcommand ──────────────────────────────────────────────────────────
 
 fn execute_list(lockfile: &Lockfile, nu_paths: &NuPaths) -> Result<()> {