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 (or report-only 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)

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
 ```
 
 ---
@@ -333,7 +333,7 @@ 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; repairs by default |
 
 ### Common flags (by command)
 

docs/numan-doctor.md

@@ -22,20 +22,20 @@ It answers: *“Is this Numan root consistent, safe to mutate, and aligned with
 ## Invocation
 
 ```text
-numan doctor [--fix] [--yes] [--json] [--nupm-home PATH]
+numan doctor [--scan] [--json] [--nupm-home PATH]
 ```
 
 | Flag | Behavior |
 |------|----------|
-| `--fix` | After reporting, apply automated repairs (see [Repair policy](#repair-policy)) |
-| `--yes` | Skip confirmation prompts for **confirm**-tier repairs (non-TTY implies `--yes` for confirm tier only) |
+| `--scan` | Report findings without applying repairs |
+
 | `--json` | Emit a single JSON object (schema versioned); no ANSI styling. With `--fix`, include `repairs` attempted/applied |
 | `--nupm-home PATH` | Override nupm home for the optional coexistence section (same resolution order as `numan nupm status`) |
 
 Global `--root` applies as for all commands.
 
-**Default (no flags):** diagnose and print findings + manual fix hints.  
-**`--fix`:** diagnose, then repair what is allowed without user-supplied data.
+**Default (no flags):** diagnose and apply available repairs, then print findings.  
+**`--scan`:** diagnose and print findings without mutating state.
 
 ## Exit codes
 

src/cli.rs

@@ -36,9 +36,9 @@ pub enum Commands {
     Remove(cmd::remove::RemoveArgs),
     /// Garbage-collect orphaned package directories
     Gc(cmd::gc::GcArgs),
-    /// Activate installed plugins with Nu
+    /// Activate installed plugins and modules with Nu
     Activate(cmd::activate::ActivateArgs),
-    /// Deactivate active modules
+    /// Deactivate active plugins and modules
     Deactivate(cmd::deactivate::DeactivateArgs),
     /// List all installed packages
     List,
@@ -54,7 +54,7 @@ pub enum Commands {
     Nupm(cmd::nupm::NupmArgs),
     /// Generate shell completion scripts
     Completions(cmd::completions::CompletionsArgs),
-    /// Diagnose Numan root health and optionally apply safe repairs
+    /// Diagnose Numan root health and apply safe repairs
     Doctor(cmd::doctor::DoctorArgs),
     /// Install optional Nushell integration helpers
     #[command(subcommand)]

src/cmd/activate.rs

@@ -25,16 +25,12 @@ pub struct ActivateArgs {
     /// Package IDs (owner/name) to activate. Omit to activate all installed inactive packages.
     pub packages: Vec<String>,
 
-    /// Skip confirmation prompts
-    #[arg(long)]
-    pub yes: bool,
-
     /// Show detailed output
     #[arg(long)]
     pub verbose: bool,
 
     /// List all installed packages and their activation status (read-only)
-    #[arg(long, conflicts_with_all = ["yes", "packages"])]
+    #[arg(long, conflicts_with = "packages")]
     pub list: bool,
 
     /// Check activation integrity for packages (read-only, no mutation)
@@ -154,16 +150,14 @@ fn execute_with_registrar_and_runner(
     };
     drop(planning_lock);
 
-    // 8. Consent table + confirmation
+    // 8. Consent table (informational only; no prompt)
     print_grouped_consent_table(
         &plugin_targets,
         &module_targets,
         managed_file_path.as_deref(),
         &nu_paths.plugin_registry_path,
     );
 
-    crate::util::confirm::confirm_or_bail("Proceed?", args.yes, "Activation cancelled.")?;
-
     // 9. Reacquire the root mutation lock after consent.
     let _lock = acquire_mutation_lock(root)?;
 
@@ -1421,7 +1415,7 @@ mod tests {
 
         let args = ActivateArgs {
             packages: vec!["owner/myscript".to_string()],
-            yes: true,
+
             verbose: false,
             list: false,
             check: false,
@@ -1501,7 +1495,7 @@ mod tests {
 
         let args = ActivateArgs {
             packages: vec!["owner/mycomp".to_string()],
-            yes: true,
+
             verbose: false,
             list: false,
             check: false,
@@ -1587,7 +1581,7 @@ mod tests {
 
         let args = ActivateArgs {
             packages: vec!["owner/mymod".to_string()],
-            yes: true,
+
             verbose: false,
             list: false,
             check: false,
@@ -1669,7 +1663,7 @@ mod tests {
 
         let args = ActivateArgs {
             packages: vec!["owner/depmod".to_string()],
-            yes: true,
+
             verbose: false,
             list: false,
             check: false,

src/cmd/deactivate.rs

@@ -39,10 +39,6 @@ pub struct DeactivateArgs {
     /// Package IDs (owner/name) to deactivate. Omit to deactivate all active plugins and modules.
     pub packages: Vec<String>,
 
-    /// Skip confirmation prompts
-    #[arg(long)]
-    pub yes: bool,
-
     /// Show detailed output
     #[arg(long)]
     pub verbose: bool,
@@ -146,11 +142,9 @@ pub fn execute_with_candidate_runner_and_unregistrar(
     }
     drop(planning_lock);
 
-    // 5. Show consent table and confirm
+    // 5. Show consent table (informational only; no prompt)
     print_consent_table(&targets_requested, &nu_paths.plugin_registry_path);
 
-    crate::util::confirm::confirm_or_bail("Proceed?", args.yes, "Deactivation cancelled.")?;
-
     // 6. Reacquire the root mutation lock after consent.
     let _lock = acquire_mutation_lock(root)?;
 
@@ -166,7 +160,7 @@ pub fn execute_with_candidate_runner_and_unregistrar(
     // on the current authoritative state.
     let mut lockfile = Lockfile::load(root)?;
     let targets_requested =
-        reclassify_confirmed_targets(args, &lockfile, root, &nu_paths, &targets_requested)?;
+        reclassify_targets(args, &lockfile, root, &nu_paths, &targets_requested)?;
     if targets_requested.is_empty() {
         println!("Nothing to deactivate.");
         return Ok(());
@@ -505,17 +499,17 @@ fn active_plugin_from_entry(
     })
 }
 
-fn reclassify_confirmed_targets(
+fn reclassify_targets(
     args: &DeactivateArgs,
     lockfile: &Lockfile,
     root: &Path,
     nu_paths: &NuPaths,
-    confirmed_targets: &ClassifiedTargets,
+    planned_targets: &ClassifiedTargets,
 ) -> Result<ClassifiedTargets> {
     let current_targets = classify_and_validate_packages(args, lockfile, root, nu_paths)?;
-    if current_targets != *confirmed_targets {
+    if current_targets != *planned_targets {
         bail!(
-            "Activation state changed after confirmation. No packages were deactivated; retry the command to review the current targets."
+            "Activation state changed since planning; no packages were deactivated. Retry to review current targets."
         );
     }
     Ok(current_targets)
@@ -1339,7 +1333,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/myplugin".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1360,7 +1354,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/myplugin".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1381,7 +1375,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec![],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1397,7 +1391,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/myplugin".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1414,7 +1408,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/myscript".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1433,7 +1427,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/mycomp".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1453,7 +1447,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/mymod".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1472,7 +1466,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/nosuchpkg".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1492,7 +1486,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/mymod".to_string()],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1552,7 +1546,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec![],
-            yes: true,
+
             verbose: false,
         };
 
@@ -1564,11 +1558,11 @@ mod tests {
     }
 
     #[test]
-    fn reclassification_rejects_expanded_implicit_targets_after_confirmation() {
+    fn reclassification_rejects_expanded_implicit_targets_after_planning() {
         let dir = TempDir::new().unwrap();
         let args = DeactivateArgs {
             packages: vec![],
-            yes: true,
+
             verbose: false,
         };
         let confirmed_lockfile = make_lockfile_with_modules(vec![("owner/alpha", "module", true)]);
@@ -1584,15 +1578,15 @@ mod tests {
             ("owner/beta", "module", true),
         ]);
 
-        let error = reclassify_confirmed_targets(
+        let error = reclassify_targets(
             &args,
             &changed_lockfile,
             dir.path(),
             &fake_nu_paths(),
             &confirmed_targets,
         )
         .unwrap_err();
-        assert!(error.to_string().contains("changed after confirmation"));
+        assert!(error.to_string().contains("changed since planning"));
     }
 
     #[test]
@@ -1614,7 +1608,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/highlight".to_string()],
-            yes: true,
+
             verbose: false,
         };
         execute_with_unregistrar(&args, env.root(), &|_nu, identity, _cfg| {
@@ -1671,7 +1665,7 @@ mod tests {
         let called = AtomicBool::new(false);
         let args = DeactivateArgs {
             packages: vec![],
-            yes: true,
+
             verbose: false,
         };
         let err = execute_with_unregistrar(&args, env.root(), &|_nu, _identity, _cfg| {
@@ -1731,7 +1725,7 @@ mod tests {
         let called = AtomicBool::new(false);
         let args = DeactivateArgs {
             packages: vec!["owner/highlight".to_string()],
-            yes: true,
+
             verbose: false,
         };
         execute_with_unregistrar(&args, env.root(), &|_nu, _identity, _cfg| {
@@ -1762,7 +1756,7 @@ mod tests {
 
         let args = DeactivateArgs {
             packages: vec!["owner/highlight".to_string()],
-            yes: true,
+
             verbose: false,
         };
         let err = execute_with_unregistrar(&args, env.root(), &|_nu, _name, _cfg| {