fix: address remaining CodeRabbit and Devin review feedback

- doctor.ts: Use getAdapter() per AgentType instead of getAllAdapters()
  spread (which destroys prototype methods like isDetected)
- doctor.ts: Use getGlobalSkillsDir() from AGENT_CONFIG instead of
  hardcoded path formula
- session-explainer.ts: Defensively default state.history and
  state.decisions to empty arrays
- session-explainer.ts: Use loadConfig().agent with skillSource fallback
  instead of always using skillSource as agent name
- observation-store.ts: Add static readAll() that reads observations
  without sessionId mismatch clearing
- session.ts: Use ObservationStore.readAll() for snapshot save to avoid
  empty observations due to sessionId mismatch

Author: rohitg00

packages/cli/src/commands/doctor.ts

@@ -3,9 +3,9 @@ import { execFileSync } from 'node:child_process';
 import { existsSync, lstatSync, readlinkSync, readdirSync, mkdirSync, unlinkSync } from 'node:fs';
 import { resolve, join } from 'node:path';
 import { homedir } from 'node:os';
-import { detectAgent, getAllAdapters, getAdapter } from '@skillkit/agents';
-import type { AgentType } from '@skillkit/core';
-import { findAllSkills, validateSkill, loadConfig, getProjectConfigPath } from '@skillkit/core';
+import { detectAgent, getAdapter } from '@skillkit/agents';
+import { AgentType, findAllSkills, validateSkill, loadConfig, getProjectConfigPath, getGlobalSkillsDir } from '@skillkit/core';
+import type { AgentType as AgentTypeT } from '@skillkit/core';
 import { getSearchDirs } from '../helpers.js';
 import { colors, symbols } from '../onboarding/index.js';
 
@@ -82,7 +82,7 @@ export class DoctorCommand extends Command {
     }
 
     // --- Agent Detection ---
-    let detectedAgent: AgentType = 'universal';
+    let detectedAgent: AgentTypeT = 'universal';
     try {
       detectedAgent = await detectAgent();
       results.push({ name: 'Detected agent', status: 'pass', message: `Detected: ${detectedAgent}` });
@@ -92,12 +92,12 @@ export class DoctorCommand extends Command {
 
     const otherDetected: string[] = [];
     try {
-      const allAdapters = getAllAdapters();
-      for (const adapter of allAdapters) {
-        if (adapter.agentType === detectedAgent || adapter.agentType === 'universal') continue;
+      for (const agentType of AgentType.options) {
+        if (agentType === detectedAgent || agentType === 'universal') continue;
         try {
-          if (await adapter.isDetected()) {
-            otherDetected.push(adapter.agentType);
+          const agentAdapter = getAdapter(agentType);
+          if (await agentAdapter.isDetected()) {
+            otherDetected.push(agentType);
           }
         } catch {
           // skip
@@ -132,8 +132,9 @@ export class DoctorCommand extends Command {
       }
     }
 
-    const globalSkillsDir = join(homedir(), `.${detectedAgent === 'claude-code' ? 'claude' : detectedAgent}`, 'skills');
-    if (existsSync(globalSkillsDir)) {
+    const globalSkillsDirRaw = getGlobalSkillsDir(detectedAgent);
+    const globalSkillsDir = globalSkillsDirRaw ? globalSkillsDirRaw.replace(/^~/, homedir()) : null;
+    if (globalSkillsDir && existsSync(globalSkillsDir)) {
       const entries = readdirSync(globalSkillsDir).filter(e => !e.startsWith('.'));
       results.push({ name: 'Global skills dir', status: 'pass', message: `${globalSkillsDir} (${entries.length} entries)` });
     } else {

packages/cli/src/commands/session.ts

@@ -360,7 +360,7 @@ export class SessionSnapshotSaveCommand extends Command {
 
     let observations: SessionSnapshot['observations'] = [];
     try {
-      const raw = new ObservationStore(projectPath).getAll();
+      const raw = ObservationStore.readAll(projectPath);
       observations = raw.map((o) => ({
         id: o.id,
         timestamp: o.timestamp,

packages/core/src/memory/observation-store.ts

@@ -181,6 +181,18 @@ export class ObservationStore {
     return this.load().observations;
   }
 
+  static readAll(projectPath: string): Observation[] {
+    const filePath = join(projectPath, '.skillkit', 'memory', 'observations.yaml');
+    if (!existsSync(filePath)) return [];
+    try {
+      const content = readFileSync(filePath, 'utf-8');
+      const data = parseYaml(content) as ObservationStoreData;
+      return data?.observations ?? [];
+    } catch {
+      return [];
+    }
+  }
+
   getByType(type: ObservationType): Observation[] {
     return this.load().observations.filter((o) => o.type === type);
   }

packages/core/src/session/session-explainer.ts

@@ -2,6 +2,7 @@ import type { SessionExplanation } from './types.js';
 import { SessionManager } from './manager.js';
 import { ObservationStore } from '../memory/observation-store.js';
 import { getGitCommits } from '../learning/git-analyzer.js';
+import { loadConfig } from '../config.js';
 
 function formatDuration(ms: number): string {
   const seconds = Math.floor(ms / 1000);
@@ -46,9 +47,21 @@ export class SessionExplainer {
       return explanation;
     }
 
+    try {
+      const configAgent = loadConfig().agent;
+      if (configAgent && configAgent !== 'universal') {
+        explanation.agent = configAgent;
+      } else if (state.currentExecution?.skillSource) {
+        explanation.agent = state.currentExecution.skillSource;
+      }
+    } catch {
+      if (state.currentExecution?.skillSource) {
+        explanation.agent = state.currentExecution.skillSource;
+      }
+    }
+
     if (state.currentExecution) {
       const exec = state.currentExecution;
-      explanation.agent = exec.skillSource || 'unknown';
 
       const startTime = new Date(exec.startedAt).getTime();
       explanation.duration = formatDuration(Date.now() - startTime);
@@ -79,7 +92,7 @@ export class SessionExplainer {
       }
     }
 
-    for (const hist of state.history) {
+    for (const hist of state.history ?? []) {
       const alreadyListed = explanation.skillsUsed.some(
         (s) => s.name === hist.skillName
       );
@@ -96,10 +109,10 @@ export class SessionExplainer {
 
     explanation.filesModified = [...new Set(explanation.filesModified)];
 
-    explanation.decisions = state.decisions.map(({ key, value }) => ({ key, value }));
+    explanation.decisions = (state.decisions ?? []).map(({ key, value }) => ({ key, value }));
 
     try {
-      const observations = new ObservationStore(this.projectPath).getAll();
+      const observations = ObservationStore.readAll(this.projectPath);
       const countByType = (type: string) => observations.filter((o) => o.type === type).length;
       explanation.observationCounts = {
         total: observations.length,