feat: add setup readiness diagnostics

crates/adaptive/README.md

@@ -26,27 +26,27 @@ framework.
 
 ## Why Use It?
 
-- ⚙️ **Install adaptive behavior through plugins**: Enable adaptive runtime
+- **Install adaptive behavior through plugins**: Enable adaptive runtime
   components through the same configuration path as other NeMo Relay plugins.
-- 📈 **Learn from observed executions**: Derive runtime hints from scope, tool,
+- **Learn from observed executions**: Derive runtime hints from scope, tool,
   and LLM events without replacing the application framework.
-- 💾 **Choose local or shared state**: Use in-memory state for local runs or the
+- **Choose local or shared state**: Use in-memory state for local runs or the
   optional Redis backend for shared persistence.
-- 🧩 **Keep adaptive behavior reusable**: Package telemetry, hint injection,
+- **Keep adaptive behavior reusable**: Package telemetry, hint injection,
   tool parallelism, and cache-governor behavior behind stable component
   settings.
 
 ## What You Get
 
-- ✅ **`AdaptiveConfig`**: A canonical config contract for the top-level
+- **`AdaptiveConfig`**: A canonical config contract for the top-level
   `adaptive` plugin component.
-- ✅ **Built-in component settings**: Typed config helpers for telemetry,
+- **Built-in component settings**: Typed config helpers for telemetry,
   adaptive hints, tool parallelism, and the Adaptive Cache Governor.
-- ✅ **State backends**: In-memory state by default and Redis-backed state behind
+- **State backends**: In-memory state by default and Redis-backed state behind
   the `redis-backend` feature.
-- ✅ **Learning primitives**: Runtime helpers and learners built on NeMo Relay
+- **Learning primitives**: Runtime helpers and learners built on NeMo Relay
   events.
-- ✅ **Adaptive Cache Governor (ACG) module surface**: The canonical
+- **Adaptive Cache Governor (ACG) module surface**: The canonical
   `nemo_relay_adaptive::acg` module for PromptIR, provider plugins, stability
   analysis, and cache telemetry normalization.
 

crates/cli/README.md

@@ -26,27 +26,28 @@ with the installed `nemo-relay` command rather than link against the crate.
 
 ## Why Use It?
 
-- 🧭 **Observe existing coding agents**: Run Claude Code, Codex, or Hermes
+- **Observe existing coding agents**: Run Claude Code, Codex, or Hermes
   Agent through a local NeMo Relay gateway without changing the agent
   itself.
-- 🛠️ **Configure hooks interactively**: Use the setup wizard to write project or
+- **Configure hooks interactively**: Use the setup wizard to write project or
   user config and install the hook files needed by supported agents.
-- 📡 **Export local sessions**: Write ATIF trajectory files, ATOF event JSONL
+- **Export local sessions**: Write ATIF trajectory files, ATOF event JSONL
   streams, or OpenInference spans from one shared config model.
-- 🩺 **Diagnose the machine**: Check config layers, agent binaries, hook status,
-  observability outputs, and shell completions with `nemo-relay doctor`.
+- **Diagnose setup readiness**: Check config layers, `plugins.toml` discovery,
+  agent binaries, persistent host-plugin installs, hook status, observability
+  outputs, and shell completions with `nemo-relay doctor`.
 
 ## What You Get
 
-- ✅ **`nemo-relay` binary**: The executable installed by the `nemo-relay-cli`
+- **`nemo-relay` binary**: The executable installed by the `nemo-relay-cli`
   Cargo package.
-- ✅ **First-run setup**: Bare `nemo-relay` launches setup when no config exists,
+- **First-run setup**: Bare `nemo-relay` launches setup when no config exists,
   then runs doctor once config is present.
-- ✅ **Agent shortcuts**: `nemo-relay claude`, `nemo-relay codex`, and
+- **Agent shortcuts**: `nemo-relay claude`, `nemo-relay codex`, and
   `nemo-relay hermes` start observed agent runs.
-- ✅ **Config-driven launch**: `nemo-relay run` resolves config, environment, and
+- **Config-driven launch**: `nemo-relay run` resolves config, environment, and
   CLI overrides for deterministic non-interactive use.
-- ✅ **Hook forwarding server**: A local gateway accepts agent hook events and
+- **Hook forwarding server**: A local gateway accepts agent hook events and
   provider-shaped OpenAI or Anthropic requests.
 
 ## Installation Options

crates/cli/src/config.rs

@@ -898,6 +898,11 @@ fn plugin_config_paths(
     implicit_plugin_config_paths(std::env::current_dir().ok().as_deref(), user_config_dir())
 }
 
+/// Returns the implicit `plugins.toml` discovery paths used by the gateway and doctor.
+pub(crate) fn default_plugin_config_paths() -> Vec<PathBuf> {
+    plugin_config_paths(None, None)
+}
+
 fn implicit_plugin_config_paths(
     cwd: Option<&std::path::Path>,
     user_config_dir: Option<PathBuf>,
@@ -1001,6 +1006,7 @@ struct PluginTomlConfig {
     value: Option<Value>,
     dynamic_plugins: Vec<ResolvedDynamicPluginConfig>,
     dynamic_plugin_policy: DynamicPluginHostPolicy,
+    contributing_sources: Vec<PathBuf>,
 }
 
 #[derive(Debug, Clone, Default, Deserialize)]
@@ -1026,6 +1032,18 @@ fn load_plugin_toml_config(
     load_plugin_toml_config_from_paths(plugin_config_paths(explicit, plugin_config_path))
 }
 
+/// Returns the physical `plugins.toml` files that contribute effective runtime or dynamic
+/// plugin configuration under the default discovery rules.
+pub(crate) fn effective_plugin_toml_sources() -> Result<Vec<PathBuf>, CliError> {
+    let Some(config) = load_plugin_toml_config(None, None)? else {
+        return Ok(Vec::new());
+    };
+    let mut sources = config.contributing_sources;
+    sources.sort();
+    sources.dedup();
+    Ok(sources)
+}
+
 fn load_plugin_toml_config_from_paths<I>(paths: I) -> Result<Option<PluginTomlConfig>, CliError>
 where
     I: IntoIterator<Item = PathBuf>,
@@ -1034,6 +1052,7 @@ where
     let mut dynamic_plugins = Vec::new();
     let mut dynamic_plugin_policy = DynamicPluginHostPolicy::default();
     let mut seen_plugin_ids = HashSet::new();
+    let mut contributing_sources = Vec::new();
     let mut runtime_documents = Vec::new();
 
     for path in &paths {
@@ -1051,6 +1070,11 @@ where
             })?;
         let resolved_plugins =
             resolve_dynamic_plugin_refs(path, &mut parsed, &mut seen_plugin_ids)?;
+        if !resolved_plugins.dynamic_plugins.is_empty()
+            || resolved_plugins.dynamic_plugin_policy != DynamicPluginHostPolicy::default()
+        {
+            contributing_sources.push(path.clone());
+        }
         dynamic_plugins.extend(resolved_plugins.dynamic_plugins);
         dynamic_plugin_policy.merge_from(resolved_plugins.dynamic_plugin_policy);
         runtime_documents.push((
@@ -1067,17 +1091,24 @@ where
         other => CliError::Config(other.to_string()),
     })?;
     match resolved {
-        Some((value, _sources)) => Ok(Some(PluginTomlConfig {
-            value: plugin_toml_runtime_value(value),
-            dynamic_plugins,
-            dynamic_plugin_policy,
-        })),
+        Some((value, sources)) => {
+            contributing_sources.extend(sources.iter().cloned());
+            contributing_sources.sort();
+            contributing_sources.dedup();
+            Ok(Some(PluginTomlConfig {
+                value: plugin_toml_runtime_value(value),
+                dynamic_plugins,
+                dynamic_plugin_policy,
+                contributing_sources,
+            }))
+        }
         None => Ok((!dynamic_plugins.is_empty()
             || dynamic_plugin_policy != DynamicPluginHostPolicy::default())
         .then_some(PluginTomlConfig {
             value: None,
             dynamic_plugins,
             dynamic_plugin_policy,
+            contributing_sources,
         })),
     }
 }
@@ -1137,12 +1168,18 @@ fn resolve_dynamic_plugin_refs(
     for dynamic in plugins.dynamic {
         let manifest_path = resolve_dynamic_manifest_path(source, &dynamic.manifest);
         let (manifest, manifest_ref) = DynamicPluginManifest::load_from_path(&manifest_path)
-            .map_err(|error| CliError::Config(error.to_string()))?;
+            .map_err(|error| {
+                CliError::Config(format!(
+                    "invalid dynamic plugin manifest referenced by {}: {error}",
+                    source.display()
+                ))
+            })?;
         let plugin_id = manifest.plugin.id.trim().to_owned();
         if !seen_plugin_ids.insert(plugin_id.clone()) {
             return Err(CliError::Config(format!(
-                "duplicate dynamic plugin id '{}' across plugins.toml sources",
-                plugin_id
+                "duplicate dynamic plugin id '{}' in {} across plugins.toml sources",
+                plugin_id,
+                source.display()
             )));
         }
         resolved.push(ResolvedDynamicPluginConfig {