feat(config)!: migrate to .atomic/settings.json with global sync

.github/workflows/publish.yml

@@ -83,9 +83,11 @@ jobs:
                   # Copy config directories (same as package.json "files" for binary distribution)
                   cp -r .claude config-staging/
                   cp -r .opencode config-staging/
+                  cp .mcp.json config-staging/
                   mkdir -p config-staging/.github
                   cp -r .github/skills config-staging/.github/
                   cp -r .github/agents config-staging/.github/
+                  cp .github/mcp-config.json config-staging/.github/
 
                   # Remove node_modules from .opencode if present
                   rm -rf config-staging/.opencode/node_modules

README.md

@@ -190,6 +190,8 @@ atomic init
 
 Select your agent. The CLI configures your project automatically.
 
+`atomic init` configures source-control-specific skills in your project (GitHub/Git or Sapling), while Atomic's baseline agents/skills are installed globally under `~/.atomic/.claude`, `~/.atomic/.opencode`, and `~/.atomic/.copilot` during install/update (including `bun install` for editable/package installs).
+
 Then start a chat session and run `/init` to generate `CLAUDE.md` and `AGENTS.md`:
 
 ```bash
@@ -211,7 +213,7 @@ During `atomic init`, you'll be prompted to select your source control system:
 | GitHub / Git          | `git`    | Pull Requests     | Most open-source projects    |
 | Sapling + Phabricator | `sl`     | Phabricator Diffs | Meta-style stacked workflows |
 
-The selection is saved to `.atomic.json` in your project root and configures the appropriate commit and code review commands for your workflow.
+The selection is saved to `.atomic/settings.json` in your project and configures the appropriate commit and code review commands for your workflow.
 
 #### Sapling + Phabricator Setup
 
@@ -507,11 +509,18 @@ atomic chat -a opencode --theme <light/dark>
 
 ## Configuration Files
 
-### `.atomic.json`
+### `.atomic/settings.json`
+
+Atomic stores project-level configuration in `.atomic/settings.json`. This file is created automatically during `atomic init`.
+
+Configuration resolution for project defaults:
+
+1. Local override: `.atomic/settings.json`
+2. Global fallback: `~/.atomic/settings.json`
 
-Atomic stores project-level configuration in `.atomic.json` at the root of your project. This file is created automatically during `atomic init`.
+Atomic no longer reads or writes `.atomic.json`.
 
-**Example `.atomic.json`:**
+**Example `.atomic/settings.json`:**
 
 ```json
 {
@@ -591,6 +600,7 @@ The uninstall command will:
 
 - Remove the Atomic binary from `~/.local/bin/atomic` (or your custom install directory)
 - Remove configuration data from `~/.local/share/atomic` (unless `--keep-config` is used)
+- Remove Atomic-managed global agent configs from `~/.atomic/.claude`, `~/.atomic/.opencode`, and `~/.atomic/.copilot` (unless `--keep-config` is used)
 - Display instructions for removing the PATH entry from your shell configuration
 
 ### Native installation (manual)
@@ -602,6 +612,7 @@ If the CLI command is not available, you can manually remove the files:
 ```bash
 rm -f ~/.local/bin/atomic
 rm -rf ~/.local/share/atomic
+rm -rf ~/.atomic/.claude ~/.atomic/.opencode ~/.atomic/.copilot
 ```
 
 If you installed to a custom directory, remove the binary from that location instead.
@@ -611,6 +622,9 @@ If you installed to a custom directory, remove the binary from that location ins
 ```powershell
 Remove-Item "$env:USERPROFILE\.local\bin\atomic.exe" -Force
 Remove-Item "$env:LOCALAPPDATA\atomic" -Recurse -Force
+Remove-Item "$env:USERPROFILE\.atomic\.claude" -Recurse -Force
+Remove-Item "$env:USERPROFILE\.atomic\.opencode" -Recurse -Force
+Remove-Item "$env:USERPROFILE\.atomic\.copilot" -Recurse -Force
 ```
 
 ### bun installation

install.ps1

@@ -15,6 +15,40 @@ $GithubRepo = "flora131/atomic"
 $BinaryName = "atomic"
 $BinDir = if ($env:ATOMIC_INSTALL_DIR) { $env:ATOMIC_INSTALL_DIR } elseif ($InstallDir) { $InstallDir } else { "${Home}\.local\bin" }
 $DataDir = if ($env:LOCALAPPDATA) { "${env:LOCALAPPDATA}\atomic" } else { "${Home}\AppData\Local\atomic" }
+$AtomicHome = "${Home}\.atomic"
+
+function Sync-GlobalAgentConfigs {
+    param([string]$SourceRoot)
+
+    $claudeDir = Join-Path $AtomicHome ".claude"
+    $opencodeDir = Join-Path $AtomicHome ".opencode"
+    $copilotDir = Join-Path $AtomicHome ".copilot"
+
+    $null = New-Item -ItemType Directory -Force -Path $claudeDir
+    $null = New-Item -ItemType Directory -Force -Path $opencodeDir
+    $null = New-Item -ItemType Directory -Force -Path $copilotDir
+
+    Copy-Item -Path (Join-Path $SourceRoot ".claude\*") -Destination $claudeDir -Recurse -Force
+    Copy-Item -Path (Join-Path $SourceRoot ".opencode\*") -Destination $opencodeDir -Recurse -Force
+    Copy-Item -Path (Join-Path $SourceRoot ".github\*") -Destination $copilotDir -Recurse -Force
+
+    $mcpConfigSource = Join-Path $SourceRoot ".mcp.json"
+    if (Test-Path $mcpConfigSource) {
+        Copy-Item -Path $mcpConfigSource -Destination (Join-Path $AtomicHome ".mcp.json") -Force
+    }
+
+    foreach ($agentDir in @($claudeDir, $opencodeDir, $copilotDir)) {
+        $skillsDir = Join-Path $agentDir "skills"
+        if (Test-Path $skillsDir) {
+            Get-ChildItem -Path $skillsDir -Directory -ErrorAction SilentlyContinue |
+                Where-Object { $_.Name -like "gh-*" -or $_.Name -like "sl-*" } |
+                ForEach-Object { Remove-Item -Recurse -Force $_.FullName -ErrorAction SilentlyContinue }
+        }
+    }
+
+    Remove-Item -Recurse -Force (Join-Path $copilotDir "workflows") -ErrorAction SilentlyContinue
+    Remove-Item -Force (Join-Path $copilotDir "dependabot.yml") -ErrorAction SilentlyContinue
+}
 
 # Colors for output
 $C_RESET = [char]27 + "[0m"
@@ -43,6 +77,7 @@ switch ($Arch) {
 Write-Info "Detected architecture: $Arch"
 Write-Info "Installing to: $BinDir"
 Write-Info "Config directory: $DataDir"
+Write-Info "Atomic home: $AtomicHome"
 
 # Create install directories
 $null = New-Item -ItemType Directory -Force -Path $BinDir
@@ -142,6 +177,9 @@ try {
     $null = New-Item -ItemType Directory -Force -Path $DataDir
     Expand-Archive -Path $TempConfig -DestinationPath $DataDir -Force
 
+    Write-Info "Syncing global agent configs to ${AtomicHome}..."
+    Sync-GlobalAgentConfigs -SourceRoot $DataDir
+
     # Verify installation
     $VersionOutput = & $BinaryPath --version 2>&1
     if ($LASTEXITCODE -ne 0) {
@@ -150,6 +188,7 @@ try {
 
     Write-Success "Installed ${BinaryName} ${Version} to ${BinaryPath}"
     Write-Success "Config files installed to ${DataDir}"
+    Write-Success "Global agent configs synced to ${AtomicHome}"
 
     # Update PATH
     if (-not $NoPathUpdate) {

install.sh

@@ -10,6 +10,7 @@ GITHUB_REPO="flora131/atomic"
 BINARY_NAME="atomic"
 BIN_DIR="${ATOMIC_INSTALL_DIR:-$HOME/.local/bin}"
 DATA_DIR="${XDG_DATA_HOME:-$HOME/.local/share}/atomic"
+ATOMIC_HOME="$HOME/.atomic"
 
 # Colors
 RED='\033[0;31m'
@@ -138,6 +139,31 @@ verify_checksum() {
     info "Checksum verified successfully"
 }
 
+# Sync bundled config templates into ~/.atomic for global discovery
+# Excludes SCM-specific skills (gh-*, sl-*), which are configured per-project via `atomic init`.
+sync_global_agent_configs() {
+    local source_root="$1"
+
+    mkdir -p "$ATOMIC_HOME/.claude" "$ATOMIC_HOME/.opencode" "$ATOMIC_HOME/.copilot"
+
+    cp -R "$source_root/.claude/." "$ATOMIC_HOME/.claude/"
+    cp -R "$source_root/.opencode/." "$ATOMIC_HOME/.opencode/"
+    cp -R "$source_root/.github/." "$ATOMIC_HOME/.copilot/"
+
+    if [[ -f "$source_root/.mcp.json" ]]; then
+        cp "$source_root/.mcp.json" "$ATOMIC_HOME/.mcp.json"
+    fi
+
+    # Remove SCM-managed skills from global config; these are project-scoped.
+    rm -rf "$ATOMIC_HOME/.claude/skills/gh-"* "$ATOMIC_HOME/.claude/skills/sl-"* 2>/dev/null || true
+    rm -rf "$ATOMIC_HOME/.opencode/skills/gh-"* "$ATOMIC_HOME/.opencode/skills/sl-"* 2>/dev/null || true
+    rm -rf "$ATOMIC_HOME/.copilot/skills/gh-"* "$ATOMIC_HOME/.copilot/skills/sl-"* 2>/dev/null || true
+
+    # Keep Copilot global config focused on skills/agents/instructions/MCP.
+    rm -rf "$ATOMIC_HOME/.copilot/workflows" 2>/dev/null || true
+    rm -f "$ATOMIC_HOME/.copilot/dependabot.yml" 2>/dev/null || true
+}
+
 # Get latest version
 get_latest_version() {
     curl -fsSL "https://api.github.com/repos/${GITHUB_REPO}/releases/latest" |
@@ -204,12 +230,16 @@ main() {
     mkdir -p "$DATA_DIR"
     tar -xzf "${tmp_dir}/${BINARY_NAME}-config.tar.gz" -C "$DATA_DIR"
 
+    info "Syncing global agent configs to ${ATOMIC_HOME}..."
+    sync_global_agent_configs "$DATA_DIR"
+
     # Verify installation
     "${BIN_DIR}/${BINARY_NAME}" --version >/dev/null 2>&1 ||
         error "Installation verification failed"
 
     success "Installed ${BINARY_NAME} ${version} to ${BIN_DIR}/${BINARY_NAME}"
     success "Config files installed to ${DATA_DIR}"
+    success "Global agent configs synced to ${ATOMIC_HOME}"
 
     # Update PATH in shell config
     if [[ ":$PATH:" != *":${BIN_DIR}:"* ]]; then

package.json

@@ -23,8 +23,10 @@
         "src",
         ".claude",
         ".opencode",
+        ".mcp.json",
         ".github/skills",
-        ".github/agents"
+        ".github/agents",
+        ".github/mcp-config.json"
     ],
     "scripts": {
         "dev": "bun run src/cli.ts",
@@ -33,7 +35,7 @@
         "typecheck": "tsc --noEmit",
         "lint": "oxlint --config=oxlint.json src",
         "lint:fix": "oxlint --config=oxlint.json --fix src",
-        "postinstall": "lefthook install"
+        "postinstall": "lefthook install && bun run src/scripts/postinstall.ts"
     },
     "devDependencies": {
         "@types/bun": "^1.3.9",

src/commands/chat.test.ts

@@ -0,0 +1,50 @@
+import { expect, test } from "bun:test";
+import { mkdtemp, mkdir, rm, writeFile } from "fs/promises";
+import { join } from "path";
+import { tmpdir } from "os";
+import { hasProjectScmSkills, shouldAutoInitChat } from "./chat.ts";
+
+async function withTempDir(run: (dir: string) => Promise<void>): Promise<void> {
+  const dir = await mkdtemp(join(tmpdir(), "atomic-chat-test-"));
+  try {
+    await run(dir);
+  } finally {
+    await rm(dir, { recursive: true, force: true });
+  }
+}
+
+test("hasProjectScmSkills returns false when skills directory has no managed SCM skills", async () => {
+  await withTempDir(async (dir) => {
+    await mkdir(join(dir, ".github", "skills", "init"), { recursive: true });
+    await writeFile(join(dir, ".github", "skills", "init", "SKILL.md"), "init", "utf-8");
+
+    await expect(hasProjectScmSkills("copilot", dir)).resolves.toBe(false);
+  });
+});
+
+test("hasProjectScmSkills returns true when managed SCM skill exists", async () => {
+  await withTempDir(async (dir) => {
+    const commitSkillPath = join(dir, ".github", "skills", "gh-commit", "SKILL.md");
+    await mkdir(join(commitSkillPath, ".."), { recursive: true });
+    await writeFile(commitSkillPath, "commit skill", "utf-8");
+
+    await expect(hasProjectScmSkills("copilot", dir)).resolves.toBe(true);
+  });
+});
+
+test("shouldAutoInitChat returns true when no managed SCM skills are configured", async () => {
+  await withTempDir(async (dir) => {
+    await mkdir(join(dir, ".claude"), { recursive: true });
+    await expect(shouldAutoInitChat("claude", dir)).resolves.toBe(true);
+  });
+});
+
+test("shouldAutoInitChat returns false when managed SCM skills are configured", async () => {
+  await withTempDir(async (dir) => {
+    const commitSkillPath = join(dir, ".claude", "skills", "sl-commit", "SKILL.md");
+    await mkdir(join(commitSkillPath, ".."), { recursive: true });
+    await writeFile(commitSkillPath, "sapling commit", "utf-8");
+
+    await expect(shouldAutoInitChat("claude", dir)).resolves.toBe(false);
+  });
+});

src/commands/chat.ts

@@ -21,6 +21,13 @@ import { pathExists } from "../utils/copy.ts";
 import { AGENT_CONFIG } from "../config.ts";
 import { initCommand } from "./init.ts";
 import { join } from "path";
+import { readdir } from "fs/promises";
+import {
+  ensureAtomicGlobalAgentConfigs,
+  isManagedScmSkillName,
+} from "../utils/atomic-global-config.ts";
+import { detectInstallationType, getConfigRoot } from "../utils/config-path.ts";
+import { prepareOpenCodeConfigDir } from "../utils/opencode-config.ts";
 
 // SDK client imports
 import {
@@ -77,7 +84,7 @@ function createClientForAgentType(agentType: AgentType): CodingAgentClient {
     case "claude":
       return createClaudeAgentClient();
     case "opencode":
-      return createOpenCodeClient();
+      return createOpenCodeClient({ directory: process.cwd() });
     case "copilot":
       return createCopilotClient();
     default:
@@ -104,6 +111,36 @@ function getTheme(themeName: "dark" | "light"): Theme {
   return themeName === "light" ? lightTheme : darkTheme;
 }
 
+/**
+ * Determine whether the selected agent already has project-level SCM skills.
+ */
+export async function hasProjectScmSkills(
+  agentType: AgentType,
+  projectRoot: string
+): Promise<boolean> {
+  const skillsDir = join(projectRoot, AGENT_CONFIG[agentType].folder, "skills");
+  if (!(await pathExists(skillsDir))) return false;
+
+  try {
+    const entries = await readdir(skillsDir, { withFileTypes: true });
+    return entries.some(
+      (entry) => entry.isDirectory() && isManagedScmSkillName(entry.name)
+    );
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Determine whether chat should auto-run init for the selected agent.
+ */
+export async function shouldAutoInitChat(
+  agentType: AgentType,
+  projectRoot: string = process.cwd()
+): Promise<boolean> {
+  return !(await hasProjectScmSkills(agentType, projectRoot));
+}
+
 // ============================================================================
 // Slash Command Handling
 // ============================================================================
@@ -170,14 +207,28 @@ export async function chatCommand(options: ChatCommandOptions = {}): Promise<num
   const effectiveReasoningEffort = getReasoningEffortPreference(agentType);
 
   const agentName = getAgentDisplayName(agentType);
+  const projectRoot = process.cwd();
+
+  if (detectInstallationType() !== "source") {
+    await ensureAtomicGlobalAgentConfigs(getConfigRoot());
+  }
+
+  if (agentType === "opencode") {
+    const mergedConfigDir = await prepareOpenCodeConfigDir({ projectRoot });
+    if (mergedConfigDir) {
+      process.env.OPENCODE_CONFIG_DIR = mergedConfigDir;
+    }
+  }
+
+  // Auto-init when project SCM skills are missing
+  if (await shouldAutoInitChat(agentType, projectRoot)) {
+    const configNotFoundMessage =
+      `Source control skills are not configured for ${agentName}. Starting interactive setup...`;
 
-  // Check if config folder exists locally
-  const configFolder = join(process.cwd(), AGENT_CONFIG[agentType].folder);
-  if (!(await pathExists(configFolder))) {
     await initCommand({
       showBanner: false,
       preSelectedAgent: agentType,
-      configNotFoundMessage: `Local configuration not found for ${agentName}. Starting interactive setup...`,
+      configNotFoundMessage,
     });
   }
 
@@ -221,7 +272,7 @@ export async function chatCommand(options: ChatCommandOptions = {}): Promise<num
       version: VERSION,
       model: displayModelName,
       tier: modelDisplayInfo.tier,
-      workingDir: process.cwd(),
+      workingDir: projectRoot,
       suggestion: 'Try "fix typecheck errors"',
       agentType,
       initialPrompt,