diff --git a/PROJECT_STATE.md b/PROJECT_STATE.md
index 6b913f0..063daef 100644
--- a/PROJECT_STATE.md
+++ b/PROJECT_STATE.md
@@ -115,7 +115,17 @@
 
 ---
 
-## H. Instructions for the Next AI Agent
+## H. Important Decisions
+
+| Decision | Reason | Alternatives Rejected |
+|---|---|---|
+| Native JSON store (`JsonStore`) over `electron-store` | `electron-store` v10 is pure ESM causing `ERR_REQUIRE_ESM` in Electron CJS main bundle; native `fs` JSON store has 0 external dependencies and 100% synchronous stability | `electron-store` v10 (rejected: ESM runtime collision) |
+| Atomic JSON store over `better-sqlite3` | Eliminates requirement for Visual Studio C++ compilers and node-gyp native compilation on target user PCs | `better-sqlite3` (rejected: requires C++ build tools) |
+| electron-vite over vanilla Vite | Direct Electron HMR and optimized dual-bundle build pipeline | Custom webpack, Create React App |
+
+---
+
+## I. Instructions for the Next AI Agent
 
 1. **Read `PROJECT_STATE.md` completely before making changes.**
 2. **Read `DESIGN.md` before modifying any UI.** Adhere strictly to the Axiom design system.
diff --git a/electron/persistence/database.ts b/electron/persistence/database.ts
index cff84aa..9e90d90 100644
--- a/electron/persistence/database.ts
+++ b/electron/persistence/database.ts
@@ -1,4 +1,4 @@
-import Store from 'electron-store'
+import { JsonStore } from './json-store'
 import { createLogger } from '../logger'
 import type { Repository } from '../../shared/types/git.types'
 
@@ -10,18 +10,14 @@ interface DatabaseSchema {
   graphLayout: Record<string, { x: number; y: number }>
 }
 
-let store: Store<DatabaseSchema> | null = null
+let store: JsonStore<DatabaseSchema> | null = null
 
-export function getDb(): Store<DatabaseSchema> {
+export function getDb(): JsonStore<DatabaseSchema> {
   if (!store) {
-    store = new Store<DatabaseSchema>({
-      name: 'flowgit-data',
-      defaults: {
-        repositories: [],
-        uiState: {},
-        graphLayout: {},
-      },
-      clearInvalidConfig: true,
+    store = new JsonStore<DatabaseSchema>('flowgit-data', {
+      repositories: [],
+      uiState: {},
+      graphLayout: {},
     })
   }
   return store
@@ -47,7 +43,7 @@ export function getRepository(id: string): Repository | null {
 
 export function upsertRepository(repo: Omit<Repository, 'remotes'>): void {
   const db = getDb()
-  const repos = db.get('repositories') ?? []
+  const repos = [...(db.get('repositories') ?? [])]
   const existingIndex = repos.findIndex(r => r.id === repo.id || r.path === repo.path)
 
   const fullRepo: Repository = {
@@ -78,7 +74,7 @@ export function removeRepository(id: string): void {
 
 export function pinRepository(id: string, pinned: boolean): void {
   const db = getDb()
-  const repos = db.get('repositories') ?? []
+  const repos = [...(db.get('repositories') ?? [])]
   const repo = repos.find(r => r.id === id)
   if (repo) {
     repo.isPinned = pinned
@@ -95,7 +91,7 @@ export function getUiState(key: string): string | null {
 
 export function setUiState(key: string, value: string): void {
   const db = getDb()
-  const state = db.get('uiState') ?? {}
+  const state = { ...(db.get('uiState') ?? {}) }
   state[key] = value
   db.set('uiState', state)
 }
diff --git a/electron/persistence/json-store.ts b/electron/persistence/json-store.ts
new file mode 100644
index 0000000..9211fb0
--- /dev/null
+++ b/electron/persistence/json-store.ts
@@ -0,0 +1,52 @@
+import { app } from 'electron'
+import { join } from 'path'
+import { readFileSync, writeFileSync, mkdirSync, existsSync } from 'fs'
+
+export class JsonStore<T extends object> {
+  private filePath: string
+  private data: T
+
+  constructor(name: string, defaults: T) {
+    let dir = ''
+    try {
+      dir = app.getPath('userData')
+    } catch {
+      dir = join(process.cwd(), '.flowgit-data')
+    }
+    mkdirSync(dir, { recursive: true })
+    this.filePath = join(dir, `${name}.json`)
+
+    if (existsSync(this.filePath)) {
+      try {
+        const raw = readFileSync(this.filePath, 'utf8')
+        this.data = { ...defaults, ...JSON.parse(raw) }
+      } catch {
+        this.data = { ...defaults }
+      }
+    } else {
+      this.data = { ...defaults }
+      this.save()
+    }
+  }
+
+  get<K extends keyof T>(key: K): T[K] {
+    return this.data[key]
+  }
+
+  set<K extends keyof T>(key: K, value: T[K]): void {
+    this.data[key] = value
+    this.save()
+  }
+
+  getAll(): T {
+    return { ...this.data }
+  }
+
+  private save(): void {
+    try {
+      writeFileSync(this.filePath, JSON.stringify(this.data, null, 2), 'utf8')
+    } catch (err) {
+      console.error(`Failed to write store to ${this.filePath}:`, err)
+    }
+  }
+}
diff --git a/electron/settings/settings-store.ts b/electron/settings/settings-store.ts
index 594586e..a3e2ff9 100644
--- a/electron/settings/settings-store.ts
+++ b/electron/settings/settings-store.ts
@@ -1,4 +1,4 @@
-import Store from 'electron-store'
+import { JsonStore } from '../persistence/json-store'
 import type { AppSettings } from '../../shared/types/ipc.types'
 
 const defaults: AppSettings = {
@@ -14,20 +14,23 @@ const defaults: AppSettings = {
   confirmDestructive: true,
 }
 
-const store = new Store<AppSettings>({
-  name: 'settings',
-  defaults,
-  clearInvalidConfig: true,
-})
+let store: JsonStore<AppSettings> | null = null
+
+function getStore(): JsonStore<AppSettings> {
+  if (!store) {
+    store = new JsonStore<AppSettings>('settings', defaults)
+  }
+  return store
+}
 
 export function getSettings(): AppSettings {
-  return store.store
+  return getStore().getAll()
 }
 
 export function getSetting<K extends keyof AppSettings>(key: K): AppSettings[K] {
-  return store.get(key)
+  return getStore().get(key)
 }
 
 export function setSetting<K extends keyof AppSettings>(key: K, value: AppSettings[K]): void {
-  store.set(key, value)
+  getStore().set(key, value)
 }
diff --git a/package.json b/package.json
index e05b2d7..547c8f6 100644
--- a/package.json
+++ b/package.json
@@ -17,9 +17,7 @@
     "dist": "npm run build && electron-builder",
     "dist:dir": "npm run build && electron-builder --dir"
   },
-  "dependencies": {
-    "electron-store": "^10.0.0"
-  },
+  "dependencies": {},
   "devDependencies": {
     "@electron-toolkit/preload": "^3.0.1",
     "@electron-toolkit/utils": "^3.0.0",