@bastani/atomic 0.5.14-0 → 0.5.15-0

package/.claude/settings.json

@@ -0,0 +1,24 @@
+{
+  "env": {
+    "CLAUDE_CODE_DISABLE_NONESSENTIAL_TRAFFIC": "1",
+    "ENABLE_LSP_TOOL": "1",
+    "CLAUDE_CODE_NO_FLICKER": "1"
+  },
+  "includeCoAuthoredBy": false,
+  "permissions": {
+    "defaultMode": "bypassPermissions"
+  },
+  "enabledPlugins": {
+    "pyright-lsp@claude-plugins-official": true,
+    "typescript-lsp@claude-plugins-official": true,
+    "gopls-lsp@claude-plugins-official": true,
+    "rust-analyzer-lsp@claude-plugins-official": true,
+    "jdtls-lsp@claude-plugins-official": true,
+    "clangd-lsp@claude-plugins-official": true,
+    "csharp-lsp@claude-plugins-official": true,
+    "php-lsp@claude-plugins-official": true,
+    "kotlin-lsp@claude-plugins-official": true,
+    "swift-lsp@claude-plugins-official": true,
+    "lua-lsp@claude-plugins-official": true
+  }
+}

package/.opencode/opencode.json

@@ -0,0 +1,10 @@
+{
+  "$schema": "https://opencode.ai/config.json",
+  "permission": "allow",
+  "mcp": {
+    "gh_grep": {
+      "type": "remote",
+      "url": "https://mcp.grep.app"
+    }
+  }
+}

package/README.md

@@ -51,7 +51,7 @@ atomic workflow -n review-to-merge -a claude
 atomic workflow -n ux-personas -a claude
 ```
 
-Each of these is a `.ts` file using Atomic's [Workflow SDK](#workflow-sdk--build-your-own-deterministic-harness). See [Build a Workflow](#5-build-a-workflow) for a working example, or read the full SDK reference below.
+Each of these is a `.ts` file using Atomic's [Workflow SDK](#workflow-sdk--build-your-own-deterministic-harness). See [Build a Workflow](#4-build-a-workflow) for a working example, or read the full SDK reference below.
 
 ---
 
@@ -64,10 +64,9 @@ Each of these is a `.ts` file using Atomic's [Workflow SDK](#workflow-sdk--build
   - [Quick Start](#quick-start)
     - [Prerequisites](#prerequisites)
     - [1. Install](#1-install)
-    - [2. Initialize Your Project](#2-initialize-your-project)
-    - [3. Generate Context Files](#3-generate-context-files)
-    - [4. Managing Sessions](#4-managing-sessions)
-    - [5. Build a Workflow](#5-build-a-workflow)
+    - [2. Generate Context Files](#2-generate-context-files)
+    - [3. Managing Sessions](#3-managing-sessions)
+    - [4. Build a Workflow](#4-build-a-workflow)
   - [Core Features](#core-features)
     - [Multi-Agent Support](#multi-agent-support)
     - [Workflow SDK — Build Your Own Deterministic Harness](#workflow-sdk--build-your-own-deterministic-harness)
@@ -88,7 +87,6 @@ Each of these is a `.ts` file using Atomic's [Workflow SDK](#workflow-sdk--build
   - [Commands Reference](#commands-reference)
     - [CLI Commands](#cli-commands)
       - [Global Flags](#global-flags)
-      - [`atomic init` Flags](#atomic-init-flags)
       - [`atomic session` Subcommands](#atomic-session-subcommands)
       - [`atomic chat` Flags](#atomic-chat-flags)
       - [`atomic workflow` Flags](#atomic-workflow-flags)
@@ -189,16 +187,7 @@ irm https://raw.githubusercontent.com/flora131/atomic/main/install.ps1 | iex
 > 4. Remove legacy skill directories: `rm -rf ~/.copilot/skills ~/.opencode/skills`
 > 5. Re-install using any of the install options above
 
-### 2. Initialize Your Project
-
-```bash
-cd your-project
-atomic init
-```
-
-Select your coding agent and source control system when prompted. The CLI configures your project automatically.
-
-### 3. Generate Context Files
+### 2. Generate Context Files
 
 Start a chat session and run `/init` to generate `CLAUDE.md` and `AGENTS.md`:
 
@@ -212,7 +201,7 @@ atomic chat -a <claude|opencode|copilot>
 
 This explores your codebase using sub-agents and generates documentation that gives coding agents the context they need.
 
-### 4. Managing Sessions
+### 3. Managing Sessions
 
 Atomic runs every chat and workflow session inside [tmux](https://github.com/tmux/tmux) on a dedicated socket, isolated from any personal tmux sessions you may have running. Use the built-in `session` commands to manage them:
 
@@ -242,7 +231,7 @@ Session names follow a predictable pattern:
 
 > **Tip:** If your terminal disconnects or you accidentally close the window, your session is still alive — just run `atomic session connect <session-name>` to pick up where you left off.
 
-### 5. Build a Workflow
+### 4. Build a Workflow
 
 Every team has a process. Atomic lets you encode it as TypeScript — chain agent sessions together, pass transcripts between them, and run the whole thing from the CLI.
 
@@ -989,7 +978,6 @@ During `atomic chat`, there is no Atomic-owned TUI — `atomic chat -a <agent>`
 
 | Command                         | Description                                                           |
 | ------------------------------- | --------------------------------------------------------------------- |
-| `atomic init`                   | Interactive project setup (agent selection, SCM choice, config sync)  |
 | `atomic chat`                   | Spawn the native agent CLI inside a tmux/psmux session                |
 | `atomic workflow`               | Run a multi-session agent workflow with the Atomic orchestrator panel |
 | `atomic workflow list`          | List available workflows, grouped by source                           |
@@ -1008,19 +996,6 @@ These flags are available on all commands:
 | `--no-banner`   | Skip ASCII banner display                  |
 | `-v, --version` | Show version number                        |
 
-#### `atomic init` Flags
-
-| Flag                 | Description                                       |
-| -------------------- | ------------------------------------------------- |
-| `-a, --agent <name>` | Pre-select agent: `claude`, `opencode`, `copilot` |
-| `-s, --scm <name>`   | Pre-select SCM: `github`, `sapling`               |
-
-```bash
-atomic init                              # Interactive setup
-atomic init -a claude -s github          # Pre-select agent and SCM
-atomic init --yes                        # Auto-confirm all prompts
-```
-
 #### `atomic session` Subcommands
 
 The `session` command is available at three levels — scoped or global:
@@ -1127,7 +1102,7 @@ Native slash commands like `/help`, `/clear`, `/compact`, `/model`, `/theme`, `/
 
 ### `.atomic/settings.json`
 
-Created automatically during `atomic init`. Resolution order:
+Resolution order:
 
 1. Local: `.atomic/settings.json`
 2. Global: `~/.atomic/settings.json`
@@ -1150,7 +1125,7 @@ Created automatically during `atomic init`. Resolution order:
 | `version`      | number | Config schema version (currently `1`)                                                                     |
 | `scm`          | string | Source control: `github` or `sapling`                                                                     |
 | `lastUpdated`  | string | ISO 8601 timestamp of the last update                                                                     |
-| `trustedPaths` | array  | Workspaces that have completed provider onboarding via `atomic init`; atomic skips re-prompting for these |
+| `trustedPaths` | array  | Workspaces that have completed provider onboarding; atomic skips re-prompting for these |
 
 > **Note:** Model selection and reasoning effort are managed by each underlying agent CLI (e.g. Claude Code's `/model`), not by Atomic itself. Atomic's chat command spawns the agent's native TUI — use the agent's own controls to pick a model or adjust reasoning effort.
 
@@ -1319,22 +1294,6 @@ $env:GITHUB_TOKEN='ghp_...'; irm https://raw.githubusercontent.com/flora131/atom
 
 </details>
 
-<details>
-<summary>Source control selection</summary>
-
-During `atomic init`, you'll select your source control system:
-
-| SCM Type              | CLI Tool | Code Review       | Use Case          |
-| --------------------- | -------- | ----------------- | ----------------- |
-| GitHub / Git          | `git`    | Pull Requests     | Most projects     |
-| Sapling + Phabricator | `sl`     | Phabricator Diffs | Stacked workflows |
-
-**Sapling + Phabricator:** Ensure `.arcconfig` exists in your repo root. Use `/sl-commit` and `/sl-submit-diff`.
-
-**Windows note:** Sapling templates use the full path `& 'C:\Program Files\Sapling\sl.exe'` to avoid conflicts with PowerShell's `sl` alias.
-
-</details>
-
 ---
 
 ## Updating & Uninstalling
@@ -1387,7 +1346,7 @@ Remove-Item -Path ".atomic" -Recurse -Force
 <details>
 <summary>Clean up global config files</summary>
 
-> **Warning:** This deletes Atomic's global settings and cached agent configs. You'll need to re-run `atomic init` in your projects after this.
+> **Warning:** This deletes Atomic's global settings and cached agent configs.
 
 **macOS / Linux:**
 
@@ -1425,13 +1384,6 @@ If agents fail to spawn on Windows, ensure the agent CLI is in your PATH. Atomic
 
 </details>
 
-<details>
-<summary>Generating CLAUDE.md / AGENTS.md</summary>
-
-`atomic init` does **not** create these files. Run `/init` inside a chat session to generate them.
-
-</details>
-
 <details>
 <summary>Sub-agent tree stuck on "Initializing..."</summary>
 

package/assets/settings.schema.json

@@ -41,6 +41,35 @@
         },
         "additionalProperties": false
       }
+    },
+    "providers": {
+      "type": "object",
+      "description": "Per-provider overrides for chatFlags and envVars. chatFlags replaces built-in defaults entirely when set; envVars are merged on top of defaults (user values win on conflict). Local .atomic/settings.json takes precedence over global ~/.atomic/settings.json.",
+      "properties": {
+        "claude": { "$ref": "#/$defs/providerOverrides" },
+        "opencode": { "$ref": "#/$defs/providerOverrides" },
+        "copilot": { "$ref": "#/$defs/providerOverrides" }
+      },
+      "additionalProperties": false
+    }
+  },
+  "$defs": {
+    "providerOverrides": {
+      "type": "object",
+      "description": "Override settings for a single provider.",
+      "properties": {
+        "chatFlags": {
+          "type": "array",
+          "items": { "type": "string" },
+          "description": "CLI flags that replace the provider's default chat flags entirely when set."
+        },
+        "envVars": {
+          "type": "object",
+          "additionalProperties": { "type": "string" },
+          "description": "Environment variables merged on top of the provider's defaults (user values win on conflict)."
+        }
+      },
+      "additionalProperties": false
     }
   },
   "additionalProperties": false

package/dist/sdk/runtime/executor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"executor.d.ts","sourceRoot":"","sources":["../../../src/sdk/runtime/executor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAKH,OAAO,KAAK,EACV,kBAAkB,EAMlB,SAAS,EAET,YAAY,EAMb,MAAM,aAAa,CAAC;AAwErB,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAS5C,MAAM,WAAW,kBAAkB;IACjC,uCAAuC;IACvC,UAAU,EAAE,kBAAkB,CAAC;IAC/B,iBAAiB;IACjB,KAAK,EAAE,SAAS,CAAC;IACjB;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAChC,qEAAqE;IACrE,YAAY,EAAE,MAAM,CAAC;IACrB,qCAAqC;IACrC,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AA0HD;;;;;;GAMG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAKzC;AAED;;;;;GAKG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAMzC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAgB9E;AAMD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAAC,IAAI,CAAC,CAyEf;AAcD,gGAAgG;AAChG,wBAAgB,UAAU,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI;IAAE,OAAO,EAAE,MAAM,CAAA;CAAE,CAOvE;AAED,wBAAgB,oBAAoB,CAAC,QAAQ,EAAE,YAAY,EAAE,GAAG,MAAM,CAkDrE;AAykBD,wBAAsB,eAAe,IAAI,OAAO,CAAC,IAAI,CAAC,CA0JrD"}
+{"version":3,"file":"executor.d.ts","sourceRoot":"","sources":["../../../src/sdk/runtime/executor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAKH,OAAO,KAAK,EACV,kBAAkB,EAMlB,SAAS,EAET,YAAY,EAMb,MAAM,aAAa,CAAC;AAqErB,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAa5C,MAAM,WAAW,kBAAkB;IACjC,uCAAuC;IACvC,UAAU,EAAE,kBAAkB,CAAC;IAC/B,iBAAiB;IACjB,KAAK,EAAE,SAAS,CAAC;IACjB;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAChC,qEAAqE;IACrE,YAAY,EAAE,MAAM,CAAC;IACrB,qCAAqC;IACrC,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAuID;;;;;;GAMG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAKzC;AAED;;;;;GAKG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAMzC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAC5B,GAAG,EAAE,MAAM,GAAG,SAAS,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAgBxB;AAMD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAAC,IAAI,CAAC,CAyEf;AAcD,gGAAgG;AAChG,wBAAgB,UAAU,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI;IAAE,OAAO,EAAE,MAAM,CAAA;CAAE,CAOvE;AAED,wBAAgB,oBAAoB,CAAC,QAAQ,EAAE,YAAY,EAAE,GAAG,MAAM,CAkDrE;AAulBD,wBAAsB,eAAe,IAAI,OAAO,CAAC,IAAI,CAAC,CA8JrD"}

package/dist/sdk/workflows/builtin/deep-research-codebase/claude/index.d.ts

@@ -17,12 +17,15 @@
  *                     │
  *                     ▼
  *   ┌──────────────────────────────────────────────────┐
- *   │  explorer-1   explorer-2   ...   explorer-N      │   (Promise.all)
+ *   │  explorer-1   explorer-2   ...   explorer-N      │   (Promise.all, headless)
  *   └──────────────────────────────────────────────────┘
  *                     │
  *                     ▼
  *                aggregator
  *
+ * Explorers run headless (in-process, no tmux window) — they are transparent
+ * to the graph, so the visible topology is: [scout, history] → aggregator.
+ *
  * Stage 1a — codebase-scout
  *   Pure-TypeScript: lists files (git ls-files), counts LOC (batched wc -l),
  *   renders a depth-bounded ASCII tree, and bin-packs directories into N

package/dist/sdk/workflows/builtin/deep-research-codebase/claude/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/claude/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;;AA4BH,wBAyOa"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/claude/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6DG;;AA4BH,wBA2Oa"}

package/dist/sdk/workflows/builtin/deep-research-codebase/copilot/index.d.ts

@@ -18,12 +18,15 @@
  *                     │
  *                     ▼
  *   ┌──────────────────────────────────────────────────┐
- *   │  explorer-1   explorer-2   ...   explorer-N      │   (Promise.all)
+ *   │  explorer-1   explorer-2   ...   explorer-N      │   (Promise.all, headless)
  *   └──────────────────────────────────────────────────┘
  *                     │
  *                     ▼
  *                aggregator
  *
+ * Explorers run headless (in-process, no tmux window) — they are transparent
+ * to the graph, so the visible topology is: [scout, history] → aggregator.
+ *
  * Copilot-specific concerns baked in:
  *
  *

package/dist/sdk/workflows/builtin/deep-research-codebase/copilot/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/copilot/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0CG;;AAuBH,wBA+La"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/copilot/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6CG;;AAuBH,wBAiMa"}

package/dist/sdk/workflows/builtin/deep-research-codebase/opencode/index.d.ts

@@ -18,12 +18,15 @@
  *                     │
  *                     ▼
  *   ┌──────────────────────────────────────────────────┐
- *   │  explorer-1   explorer-2   ...   explorer-N      │   (Promise.all)
+ *   │  explorer-1   explorer-2   ...   explorer-N      │   (Promise.all, headless)
  *   └──────────────────────────────────────────────────┘
  *                     │
  *                     ▼
  *                aggregator
  *
+ * Explorers run headless (in-process, no tmux window) — they are transparent
+ * to the graph, so the visible topology is: [scout, history] → aggregator.
+ *
  * OpenCode-specific concerns baked in:
  *
  *  • F5 — every `ctx.stage()` call is a FRESH session with no memory of

package/dist/sdk/workflows/builtin/deep-research-codebase/opencode/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/opencode/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6CG;;AAuBH,wBA2Na"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/opencode/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgDG;;AAuBH,wBA6Na"}

package/dist/services/config/atomic-config.d.ts

@@ -0,0 +1,44 @@
+/**
+ * Atomic configuration file utilities for persisting project settings.
+ *
+ * Project/source-control selections are stored in `.atomic/settings.json`.
+ * Resolution order:
+ * 1) local `.atomic/settings.json` (project override)
+ * 2) global `~/.atomic/settings.json` (default fallback)
+ */
+import { type SourceControlType, type AgentKey, type ProviderOverrides } from "./index.ts";
+/**
+ * Atomic project configuration schema.
+ */
+export interface AtomicConfig {
+    /** Version of config schema */
+    version?: number;
+    /** Selected source control type */
+    scm?: SourceControlType;
+    /** Timestamp of last init */
+    lastUpdated?: string;
+    /** Per-provider overrides for chatFlags and envVars */
+    providers?: Partial<Record<AgentKey, ProviderOverrides>>;
+}
+/**
+ * Read atomic config with local override semantics.
+ */
+export declare function readAtomicConfig(projectDir: string): Promise<AtomicConfig | null>;
+/**
+ * Save project config to `.atomic/settings.json`.
+ */
+export declare function saveAtomicConfig(projectDir: string, updates: Partial<AtomicConfig>): Promise<void>;
+/**
+ * Get selected SCM using local override + global fallback.
+ */
+export declare function getSelectedScm(projectDir: string): Promise<SourceControlType | null>;
+/**
+ * Resolve provider overrides from global + local settings (local wins).
+ *
+ * Returns `{ chatFlags, envVars }` that are meant to be layered on top
+ * of the provider's hardcoded defaults:
+ * - `chatFlags`: when set, replaces the provider's default chat_flags entirely
+ * - `envVars`: merged on top of the provider's default env_vars (user values win)
+ */
+export declare function getProviderOverrides(agentKey: AgentKey, projectDir: string): Promise<ProviderOverrides>;
+//# sourceMappingURL=atomic-config.d.ts.map

package/dist/services/config/atomic-config.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"atomic-config.d.ts","sourceRoot":"","sources":["../../../src/services/config/atomic-config.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,EAAE,KAAK,iBAAiB,EAAE,KAAK,QAAQ,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAO3F;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,+BAA+B;IAC/B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,mCAAmC;IACnC,GAAG,CAAC,EAAE,iBAAiB,CAAC;IACxB,6BAA6B;IAC7B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,uDAAuD;IACvD,SAAS,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC,CAAC;CAC1D;AA2HD;;GAEG;AACH,wBAAsB,gBAAgB,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,GAAG,IAAI,CAAC,CAMvF;AAED;;GAEG;AACH,wBAAsB,gBAAgB,CACpC,UAAU,EAAE,MAAM,EAClB,OAAO,EAAE,OAAO,CAAC,YAAY,CAAC,GAC7B,OAAO,CAAC,IAAI,CAAC,CAsBf;AAED;;GAEG;AACH,wBAAsB,cAAc,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC,CAG1F;AAED;;;;;;;GAOG;AACH,wBAAsB,oBAAoB,CACxC,QAAQ,EAAE,QAAQ,EAClB,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,iBAAiB,CAAC,CAG5B"}

package/dist/services/config/definitions.d.ts

@@ -26,6 +26,18 @@ export interface AgentConfig {
 declare const AGENT_KEYS: readonly ["claude", "opencode", "copilot"];
 export type AgentKey = (typeof AGENT_KEYS)[number];
 export declare const AGENT_CONFIG: Record<AgentKey, AgentConfig>;
+/**
+ * Per-provider overrides that users can set in `.atomic/settings.json`
+ * (local) or `~/.atomic/settings.json` (global).
+ *
+ * - `chatFlags`: when set, replaces the agent's default `chat_flags` entirely.
+ * - `envVars`: environment variables merged on top of the agent's default
+ *   `env_vars` (user values win on conflict).
+ */
+export interface ProviderOverrides {
+    chatFlags?: string[];
+    envVars?: Record<string, string>;
+}
 export declare function isValidAgent(key: string): key is AgentKey;
 export declare function getAgentConfig(key: AgentKey): AgentConfig;
 export declare function getAgentKeys(): AgentKey[];
@@ -37,26 +49,16 @@ declare const SCM_KEYS: readonly ["github", "sapling"];
 /** Supported source control types — derived from SCM_KEYS tuple. */
 export type SourceControlType = (typeof SCM_KEYS)[number];
 export interface ScmConfig {
-    /** Internal identifier */
-    name: string;
     /** Display name for prompts */
     displayName: string;
     /** Primary CLI tool (git or sl) */
     cliTool: string;
-    /** Code review tool (gh, jf submit, arc diff, etc.) */
-    reviewTool: string;
     /** Code review system (github, phabricator) */
     reviewSystem: string;
-    /** Directory marker for potential future auto-detection */
+    /** Directory marker used to detect this SCM in a repo (e.g. `.git`, `.sl`) */
     detectDir: string;
-    /** Code review command file name */
-    reviewCommandFile: string;
-    /** Required configuration files */
-    requiredConfigFiles?: string[];
 }
 export declare const SCM_CONFIG: Record<SourceControlType, ScmConfig>;
-/** Commands that have SCM-specific variants */
-export declare const SCM_SPECIFIC_COMMANDS: string[];
 /**
  * SCM-variant skill names, grouped by source control type.
  *
@@ -78,8 +80,11 @@ export declare function getScmKeys(): SourceControlType[];
  */
 export declare function isValidScm(key: string): key is SourceControlType;
 /**
- * Get the configuration for a specific SCM type
+ * Detect the SCM type by looking for marker directories in `projectRoot`.
+ *
+ * Checks each {@link ScmConfig.detectDir} (e.g. `.git`, `.sl`) and returns
+ * the first match. Returns `null` when no known marker is found.
  */
-export declare function getScmConfig(key: SourceControlType): ScmConfig;
+export declare function detectScmType(projectRoot: string): Promise<SourceControlType | null>;
 export {};
 //# sourceMappingURL=definitions.d.ts.map

package/dist/services/config/definitions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"definitions.d.ts","sourceRoot":"","sources":["../../../src/services/config/definitions.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,MAAM,WAAW,WAAW;IAC1B,iCAAiC;IACjC,IAAI,EAAE,MAAM,CAAC;IACb,mCAAmC;IACnC,GAAG,EAAE,MAAM,CAAC;IACZ,kEAAkE;IAClE,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,qFAAqF;IACrF,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,0CAA0C;IAC1C,MAAM,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,WAAW,EAAE,MAAM,CAAC;IACpB,yDAAyD;IACzD,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,qEAAqE;IACrE,gBAAgB,EAAE,KAAK,CAAC;QACtB,MAAM,EAAE,MAAM,CAAC;QACf,WAAW,EAAE,MAAM,CAAC;QACpB,KAAK,EAAE,OAAO,CAAC;KAChB,CAAC,CAAC;CACJ;AAED,QAAA,MAAM,UAAU,4CAA6C,CAAC;AAC9D,MAAM,MAAM,QAAQ,GAAG,CAAC,OAAO,UAAU,CAAC,CAAC,MAAM,CAAC,CAAC;AAEnD,eAAO,MAAM,YAAY,EAAE,MAAM,CAAC,QAAQ,EAAE,WAAW,CA2EtD,CAAC;AAEF,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,IAAI,QAAQ,CAEzD;AAED,wBAAgB,cAAc,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAEzD;AAED,wBAAgB,YAAY,IAAI,QAAQ,EAAE,CAEzC;AAED;;GAEG;AAEH,6BAA6B;AAC7B,QAAA,MAAM,QAAQ,gCAAiC,CAAC;AAEhD,oEAAoE;AACpE,MAAM,MAAM,iBAAiB,GAAG,CAAC,OAAO,QAAQ,CAAC,CAAC,MAAM,CAAC,CAAC;AAE1D,MAAM,WAAW,SAAS;IACxB,0BAA0B;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,+BAA+B;IAC/B,WAAW,EAAE,MAAM,CAAC;IACpB,mCAAmC;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,uDAAuD;IACvD,UAAU,EAAE,MAAM,CAAC;IACnB,+CAA+C;IAC/C,YAAY,EAAE,MAAM,CAAC;IACrB,2DAA2D;IAC3D,SAAS,EAAE,MAAM,CAAC;IAClB,oCAAoC;IACpC,iBAAiB,EAAE,MAAM,CAAC;IAC1B,mCAAmC;IACnC,mBAAmB,CAAC,EAAE,MAAM,EAAE,CAAC;CAChC;AAED,eAAO,MAAM,UAAU,EAAE,MAAM,CAAC,iBAAiB,EAAE,SAAS,CAoB3D,CAAC;AAEF,+CAA+C;AAC/C,eAAO,MAAM,qBAAqB,UAAa,CAAC;AAEhD;;;;;;;;GAQG;AACH,eAAO,MAAM,kBAAkB,EAAE,MAAM,CAAC,iBAAiB,EAAE,SAAS,MAAM,EAAE,CAIzE,CAAC;AAEJ,4EAA4E;AAC5E,eAAO,MAAM,cAAc,EAAE,SAAS,MAAM,EAG3C,CAAC;AAEF;;GAEG;AACH,wBAAgB,UAAU,IAAI,iBAAiB,EAAE,CAEhD;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,IAAI,iBAAiB,CAEhE;AAED;;GAEG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,iBAAiB,GAAG,SAAS,CAE9D"}
+{"version":3,"file":"definitions.d.ts","sourceRoot":"","sources":["../../../src/services/config/definitions.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,MAAM,WAAW,WAAW;IAC1B,iCAAiC;IACjC,IAAI,EAAE,MAAM,CAAC;IACb,mCAAmC;IACnC,GAAG,EAAE,MAAM,CAAC;IACZ,kEAAkE;IAClE,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,qFAAqF;IACrF,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,0CAA0C;IAC1C,MAAM,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,WAAW,EAAE,MAAM,CAAC;IACpB,yDAAyD;IACzD,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,qEAAqE;IACrE,gBAAgB,EAAE,KAAK,CAAC;QACtB,MAAM,EAAE,MAAM,CAAC;QACf,WAAW,EAAE,MAAM,CAAC;QACpB,KAAK,EAAE,OAAO,CAAC;KAChB,CAAC,CAAC;CACJ;AAED,QAAA,MAAM,UAAU,4CAA6C,CAAC;AAC9D,MAAM,MAAM,QAAQ,GAAG,CAAC,OAAO,UAAU,CAAC,CAAC,MAAM,CAAC,CAAC;AAEnD,eAAO,MAAM,YAAY,EAAE,MAAM,CAAC,QAAQ,EAAE,WAAW,CA4DtD,CAAC;AAEF;;;;;;;GAOG;AACH,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAClC;AAED,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,IAAI,QAAQ,CAEzD;AAED,wBAAgB,cAAc,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAEzD;AAED,wBAAgB,YAAY,IAAI,QAAQ,EAAE,CAEzC;AAED;;GAEG;AAEH,6BAA6B;AAC7B,QAAA,MAAM,QAAQ,gCAAiC,CAAC;AAEhD,oEAAoE;AACpE,MAAM,MAAM,iBAAiB,GAAG,CAAC,OAAO,QAAQ,CAAC,CAAC,MAAM,CAAC,CAAC;AAE1D,MAAM,WAAW,SAAS;IACxB,+BAA+B;IAC/B,WAAW,EAAE,MAAM,CAAC;IACpB,mCAAmC;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,+CAA+C;IAC/C,YAAY,EAAE,MAAM,CAAC;IACrB,8EAA8E;IAC9E,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,eAAO,MAAM,UAAU,EAAE,MAAM,CAAC,iBAAiB,EAAE,SAAS,CAa3D,CAAC;AAEF;;;;;;;;GAQG;AACH,eAAO,MAAM,kBAAkB,EAAE,MAAM,CAAC,iBAAiB,EAAE,SAAS,MAAM,EAAE,CAIzE,CAAC;AAEJ,4EAA4E;AAC5E,eAAO,MAAM,cAAc,EAAE,SAAS,MAAM,EAG3C,CAAC;AAEF;;GAEG;AACH,wBAAgB,UAAU,IAAI,iBAAiB,EAAE,CAEhD;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,IAAI,iBAAiB,CAEhE;AAED;;;;;GAKG;AACH,wBAAsB,aAAa,CACjC,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC,CAWnC"}

package/dist/services/config/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Configuration Module Exports
+ *
+ * Centralized access to the CLI's agent and SCM configuration.
+ */
+export * from "./definitions.ts";
+//# sourceMappingURL=index.d.ts.map

package/dist/services/config/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/services/config/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,cAAc,kBAAkB,CAAC"}

package/dist/services/config/settings-schema.d.ts

@@ -0,0 +1,2 @@
+export declare const SETTINGS_SCHEMA_URL = "https://raw.githubusercontent.com/flora131/atomic/main/assets/settings.schema.json";
+//# sourceMappingURL=settings-schema.d.ts.map

package/dist/services/config/settings-schema.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"settings-schema.d.ts","sourceRoot":"","sources":["../../../src/services/config/settings-schema.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,mBAAmB,uFACsD,CAAC"}

package/dist/services/system/copy.d.ts

@@ -1,6 +1,7 @@
 /**
  * Utilities for copying directories and files with exclusions
  */
+import type { Ignore } from "ignore";
 /**
  * Safely create a directory (and parents) without throwing on EEXIST.
  *
@@ -31,6 +32,8 @@ export declare function isPathSafe(basePath: string, targetPath: string): boolea
 interface CopyOptions {
     /** Paths to exclude (relative to source root or base names) */
     exclude?: string[];
+    /** Gitignore-style filter for common junk patterns (via the `ignore` package) */
+    ignoreFilter?: Ignore;
     /** Whether to skip scripts for the opposite platform */
     skipOppositeScripts?: boolean;
 }
@@ -43,8 +46,12 @@ export declare function copyFile(src: string, dest: string): Promise<void>;
  * Check if a path should be excluded based on exclusion rules.
  * Uses normalized paths (forward slashes) to ensure consistent matching
  * on both Windows and Unix systems.
+ *
+ * When an {@link Ignore} filter is provided, gitignore-style glob patterns
+ * are evaluated first so common junk files (.DS_Store, node_modules, etc.)
+ * are filtered automatically without polluting the explicit `exclude` list.
  */
-export declare function shouldExclude(relativePath: string, name: string, exclude: string[]): boolean;
+export declare function shouldExclude(relativePath: string, name: string, exclude: string[], ignoreFilter?: Ignore): boolean;
 /**
  * Recursively copy a directory, overwriting existing destination files.
  */

package/dist/services/system/copy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"copy.d.ts","sourceRoot":"","sources":["../../../src/services/system/copy.ts"],"names":[],"mappings":"AAAA;;GAEG;AAYH;;;;;;;GAOG;AACH,wBAAsB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAa3D;AAED;;GAEG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAahD;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C;AAED;;;GAGG;AACH,wBAAgB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,OAAO,CAGxE;AAED,UAAU,WAAW;IACnB,+DAA+D;IAC/D,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,wDAAwD;IACxD,mBAAmB,CAAC,EAAE,OAAO,CAAC;CAC/B;AAED;;;GAGG;AACH,wBAAsB,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAYvE;AAyDD;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EAAE,GAChB,OAAO,CAsBT;AA+GD;;GAEG;AACH,wBAAsB,OAAO,CAC3B,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,OAAO,GAAE,WAAgB,EACzB,OAAO,CAAC,EAAE,MAAM,EAChB,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,IAAI,CAAC,CAEf;AAED;;GAEG;AACH,wBAAsB,qBAAqB,CACzC,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,OAAO,GAAE,WAAgB,EACzB,OAAO,CAAC,EAAE,MAAM,EAChB,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,IAAI,CAAC,CAEf;AAED;;GAEG;AACH,wBAAsB,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAO/D;AAED;;GAEG;AACH,wBAAsB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAOhE;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAqBhE"}
+{"version":3,"file":"copy.d.ts","sourceRoot":"","sources":["../../../src/services/system/copy.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAQrC;;;;;;;GAOG;AACH,wBAAsB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAa3D;AAED;;GAEG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAahD;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C;AAED;;;GAGG;AACH,wBAAgB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,OAAO,CAGxE;AAED,UAAU,WAAW;IACnB,+DAA+D;IAC/D,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,iFAAiF;IACjF,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,wDAAwD;IACxD,mBAAmB,CAAC,EAAE,OAAO,CAAC;CAC/B;AAED;;;GAGG;AACH,wBAAsB,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAYvE;AAyDD;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAC3B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EAAE,EACjB,YAAY,CAAC,EAAE,MAAM,GACpB,OAAO,CAyBT;AA+GD;;GAEG;AACH,wBAAsB,OAAO,CAC3B,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,OAAO,GAAE,WAAgB,EACzB,OAAO,CAAC,EAAE,MAAM,EAChB,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,IAAI,CAAC,CAEf;AAED;;GAEG;AACH,wBAAsB,qBAAqB,CACzC,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,OAAO,GAAE,WAAgB,EACzB,OAAO,CAAC,EAAE,MAAM,EAChB,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,IAAI,CAAC,CAEf;AAED;;GAEG;AACH,wBAAsB,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAO/D;AAED;;GAEG;AACH,wBAAsB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAOhE;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAqBhE"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/atomic",
-  "version": "0.5.14-0",
+  "version": "0.5.15-0",
   "description": "Configuration management CLI and SDK for coding agents",
   "type": "module",
   "license": "MIT",
@@ -45,7 +45,9 @@
     "assets/settings.schema.json",
     ".agents/skills",
     ".claude/agents",
+    ".claude/settings.json",
     ".opencode/agents",
+    ".opencode/opencode.json",
     ".github/agents",
     ".github/lsp.json"
   ],

package/src/cli.ts

@@ -5,10 +5,6 @@
  * Built with Commander.js for robust argument parsing and type-safe options.
  *
  * Usage:
- *   atomic                                    Interactive setup (same as 'atomic init')
- *   atomic init                               Interactive setup with agent selection
- *   atomic init -a <agent>                    Setup specific agent (skip selection)
- *   atomic init -s <scm>                      Setup specific SCM (github, sapling)
  *   atomic chat -a <agent>                    Start interactive chat with an agent
  *   atomic chat session list                  List running chat/workflow sessions
  *   atomic chat session connect <id>          Attach to a session
@@ -25,7 +21,7 @@
 import { Command } from "@commander-js/extra-typings";
 import { VERSION } from "./version.ts";
 import { COLORS } from "./theme/colors.ts";
-import { AGENT_CONFIG, type AgentKey, SCM_CONFIG, type SourceControlType } from "./services/config/index.ts";
+import { AGENT_CONFIG, type AgentKey } from "./services/config/index.ts";
 import { SUPPORTED_SHELLS, type Shell } from "./completions/index.ts";
 
 // ─── Session subcommand factory ─────────────────────────────────────────────
@@ -114,31 +110,6 @@ export function createProgram() {
 
     // Build agent choices string for help text
     const agentChoices = Object.keys(AGENT_CONFIG).join(", ");
-    const scmChoices = Object.keys(SCM_CONFIG).join(", ");
-
-    // Add init command
-    program
-        .command("init")
-        .description("Interactive setup with agent selection")
-        .option(
-            "-a, --agent <name>",
-            `Pre-select agent to configure (${agentChoices})`,
-        )
-        .option(
-            "-s, --scm <name>",
-            `Pre-select source control system (${scmChoices})`,
-        )
-        .action(async (localOpts) => {
-            const globalOpts = program.opts();
-            const { initCommand } = await import("./commands/cli/init.ts");
-
-            await initCommand({
-                showBanner: globalOpts.banner !== false,
-                preSelectedAgent: localOpts.agent as AgentKey | undefined,
-                preSelectedScm: localOpts.scm as SourceControlType | undefined,
-                yes: globalOpts.yes,
-            });
-        });
 
     // ── Chat command (default) ──────────────────────────────────────────────
     const chatCmd = program

package/src/commands/cli/chat/index.ts

@@ -17,6 +17,8 @@ import { join } from "node:path";
 import { homedir } from "node:os";
 import { mkdir, writeFile, rm } from "node:fs/promises";
 import { AGENT_CONFIG, type AgentKey } from "../../../services/config/index.ts";
+import { getProviderOverrides } from "../../../services/config/atomic-config.ts";
+import { ensureProjectSetup } from "../init/index.ts";
 import { COLORS } from "../../../theme/colors.ts";
 import { isCommandInstalled } from "../../../services/system/detect.ts";
 import {
@@ -66,12 +68,21 @@ export function getAgentDisplayName(agentType: AgentType): string {
 /**
  * Build the argv array for spawning the agent CLI.
  *
- * Starts with the agent's default chat_flags, then appends any
- * extra args the user passed after `-a <agent>`.
+ * Starts with the agent's default chat_flags (or replaces them entirely
+ * when the user sets `chatFlags` in `.atomic/settings.json`), then
+ * appends any extra args the user passed after `-a <agent>`.
  */
-export function buildAgentArgs(agentType: AgentType, passthroughArgs: string[] = []): string[] {
+export async function buildAgentArgs(
+  agentType: AgentType,
+  passthroughArgs: string[] = [],
+  projectRoot: string = process.cwd(),
+): Promise<string[]> {
   const config = AGENT_CONFIG[agentType];
-  return [...config.chat_flags, ...passthroughArgs];
+  const overrides = await getProviderOverrides(agentType, projectRoot);
+
+  const flags = overrides.chatFlags ?? [...config.chat_flags];
+
+  return [...flags, ...passthroughArgs];
 }
 
 function generateChatId(): string {
@@ -172,10 +183,14 @@ export async function chatCommand(options: ChatCommandOptions = {}): Promise<num
 
   await ensureAtomicGlobalAgentConfigs(configRoot);
 
+  // ── Preflight: project setup (onboarding files, skills, trusted workspace) ──
+  await ensureProjectSetup(agentType, projectRoot);
+
   // ── Build argv ──
-  const args = buildAgentArgs(agentType, passthroughArgs);
+  const args = await buildAgentArgs(agentType, passthroughArgs, projectRoot);
   const cmd = [config.cmd, ...args];
-  const envVars = config.env_vars;
+  const overrides = await getProviderOverrides(agentType, projectRoot);
+  const envVars = { ...config.env_vars, ...overrides.envVars };
 
   // ── No TTY: tmux attach requires a real terminal ──
   if (!process.stdin.isTTY) {