refactor(config): remove SCM detection and per-SCM skill installation

.mcp.json

@@ -3,7 +3,7 @@
     "github": {
       "type": "http",
       "url": "https://api.githubcopilot.com/mcp",
-      "headers": { "Authorization": "Bearer YOUR_GITHUB_PAT" }
+      "headers": { "Authorization": "Bearer ${GITHUB_PERSONAL_ACCESS_TOKEN}" }
     }
   }
 }

.opencode/opencode.json

@@ -5,7 +5,9 @@
     "github": {
       "type": "remote",
       "url": "https://api.githubcopilot.com/mcp",
-      "headers": { "Authorization": "Bearer YOUR_GITHUB_PAT" }
+      "headers": {
+        "Authorization": "Bearer ${env:GITHUB_PERSONAL_ACCESS_TOKEN}"
+      }
     }
   }
 }

src/commands/cli/init/index.ts

@@ -1,106 +1,26 @@
 /**
  * Automatic project setup — replaces the interactive `atomic init` command.
  *
- * Detects the repo's SCM, applies onboarding files (MCP configs, settings),
- * registers the workspace as trusted, and installs SCM-specific skills.
- *
- * Called transparently during `atomic chat` preflight so users never need
- * to think about initialization.
+ * Applies onboarding files (MCP configs, settings) and registers the
+ * workspace as trusted. Called transparently during `atomic chat` preflight
+ * so users never need to think about initialization.
  */
 
-import { join, resolve } from "node:path";
-import {
-  AGENT_CONFIG,
-  type AgentKey,
-  type SourceControlType,
-  SCM_SKILLS_BY_TYPE,
-  detectScmType,
-} from "../../../services/config/index.ts";
-import { pathExists } from "../../../services/system/copy.ts";
+import { resolve } from "node:path";
+import type { AgentKey } from "../../../services/config/index.ts";
 import { getConfigRoot } from "../../../services/config/config-path.ts";
 import { upsertTrustedWorkspacePath } from "../../../services/config/settings.ts";
 import { applyManagedOnboardingFiles } from "./onboarding.ts";
-import { installLocalScmSkills, syncProjectScmSkills } from "./scm.ts";
 
 /**
- * Check whether all expected SCM skills are already present on disk.
- */
-async function areScmSkillsInstalled(
-  agentKey: AgentKey,
-  projectRoot: string,
-  scmType: SourceControlType,
-): Promise<boolean> {
-  const skillNames = SCM_SKILLS_BY_TYPE[scmType];
-  const skillsDir = join(projectRoot, AGENT_CONFIG[agentKey].folder, "skills");
-
-  for (const name of skillNames) {
-    if (!(await pathExists(join(skillsDir, name)))) {
-      return false;
-    }
-  }
-  return true;
-}
-
-function isInstalledPackage(): boolean {
-  return import.meta.dir.includes("node_modules");
-}
-
-/**
- * Ensure the project is configured for the given agent.
- *
- * Idempotent — safe to call on every `atomic chat` invocation. Expensive
- * operations (skill installation via `bunx skills add`) are skipped when
- * the skills are already present on disk. Onboarding file merges are
- * always applied since they are cheap and self-healing.
- *
- * Errors in skill installation are swallowed so the agent can still launch.
+ * Ensure the project is configured for the given agent. Idempotent — safe
+ * to call on every `atomic chat` invocation.
  */
 export async function ensureProjectSetup(
   agentKey: AgentKey,
   projectRoot: string,
 ): Promise<void> {
   const configRoot = getConfigRoot();
-  const detectedScm = await detectScmType(projectRoot);
-
-  // Apply onboarding files (idempotent merge, SCM-gated entries handled internally)
   await applyManagedOnboardingFiles(agentKey, projectRoot, configRoot);
-
-  // Register trusted workspace
   await upsertTrustedWorkspacePath(resolve(projectRoot), agentKey);
-
-  // Install SCM skills if detected and not yet present (best-effort)
-  if (detectedScm) {
-    try {
-      const alreadyInstalled = await areScmSkillsInstalled(
-        agentKey,
-        projectRoot,
-        detectedScm,
-      );
-      if (!alreadyInstalled) {
-        if (isInstalledPackage()) {
-          // npm/bunx install: fetch via the skills CLI
-          await installLocalScmSkills({
-            scmType: detectedScm,
-            agentKey,
-            cwd: projectRoot,
-          });
-        } else {
-          // Source checkout (e.g. `bun run dev`): copy from the canonical
-          // `.agents/skills` directory so prompt edits in-repo flow through
-          // to the target project without needing a publish or git push.
-          await syncProjectScmSkills({
-            scmType: detectedScm,
-            sourceSkillsDir: join(configRoot, ".agents", "skills"),
-            targetSkillsDir: join(
-              projectRoot,
-              AGENT_CONFIG[agentKey].folder,
-              "skills",
-            ),
-          });
-        }
-      }
-    } catch {
-      // Skills installation is best-effort — don't block the agent launch
-    }
-  }
 }

src/completions/bash.ts

@@ -10,7 +10,6 @@ _atomic_completions() {
 
     local commands="init chat workflow session config completions"
     local agents="claude opencode copilot"
-    local scms="github sapling"
     local global_opts="-y --yes --no-banner -v --version -h --help"
 
     # Walk the words to find the command chain (skip flags and their values)
@@ -19,8 +18,8 @@ _atomic_completions() {
     while [[ $i -lt $cword ]]; do
         local w="\${words[$i]}"
         case "$w" in
-            -a|--agent|-s|--scm|-n|--name) (( i++ )) ;;  # skip flag value
-            -*)                            ;;              # skip other flags
+            -a|--agent|-n|--name) (( i++ )) ;;  # skip flag value
+            -*)                   ;;              # skip other flags
             *)
                 if [[ -z "$cmd1" ]]; then cmd1="$w"
                 elif [[ -z "$cmd2" ]]; then cmd2="$w"
@@ -37,10 +36,6 @@ _atomic_completions() {
             COMPREPLY=( $(compgen -W "$agents" -- "$cur") )
             return
             ;;
-        -s|--scm)
-            COMPREPLY=( $(compgen -W "$scms" -- "$cur") )
-            return
-            ;;
     esac
 
     # Top-level (no subcommand yet)
@@ -51,7 +46,7 @@ _atomic_completions() {
 
     case "$cmd1" in
         init)
-            COMPREPLY=( $(compgen -W "-a --agent -s --scm -h --help" -- "$cur") )
+            COMPREPLY=( $(compgen -W "-a --agent -h --help" -- "$cur") )
             ;;
         chat)
             if [[ -z "$cmd2" ]]; then

src/completions/fish.ts

@@ -11,7 +11,6 @@ complete -c atomic -f
 # ── Helpers ─────────────────────────────────────────────────────────────────
 
 set -l agents claude opencode copilot
-set -l scms github sapling
 
 # Condition helpers — true when the command line matches a specific depth.
 # "__fish_seen_subcommand_from X" is true once token X has appeared.
@@ -36,7 +35,7 @@ function __atomic_using_cmd
                     set idx (math $idx + 1)
                     # Skip flag value for known value-flags
                     switch $tokens[(math $idx - 1)]
-                        case -a --agent -s --scm -n --name
+                        case -a --agent -n --name
                             set idx (math $idx + 1)
                     end
                 case '*'
@@ -78,7 +77,6 @@ complete -c atomic -n __atomic_no_subcommand -a completions -d 'Output shell com
 # ── init ────────────────────────────────────────────────────────────────────
 
 complete -c atomic -n '__atomic_using_cmd init' -s a -l agent -d 'Agent to configure' -r -a "$agents"
-complete -c atomic -n '__atomic_using_cmd init' -s s -l scm -d 'Source control system' -r -a "$scms"
 
 # ── chat ────────────────────────────────────────────────────────────────────