feat(system): Fix doctor action messages (remove setup.sh refs) + expand scaffold startup protocol (.trinity, inbox, init_report)

Co-Authored-By: @devpulse <devpulse@aipass>

src/aipass/aipass/apps/handlers/init/scaffold_content.py

@@ -67,6 +67,12 @@ def claude_md(name: str) -> str:
         "and respond with the status.\n"
         "\n"
         f"**Read:** `{name}_REGISTRY.json`, `README.md`, `STATUS.local.md`\n"
+        "**Read:** `.trinity/passport.json`, `.trinity/local.json`, `.trinity/observations.json`\n"
+        "**Check:** If `.ai_mail.local/inbox.json` exists, read it. Process any mail.\n"
+        "**Check:** If `dropbox/init_report.json` exists, read it — this is your birth certificate. "
+        "Use it to understand your role, the project context, and any setup instructions. "
+        "If it mentions missing provider settings (hooks, env vars, permissions), "
+        "tell the user what needs configuring and where.\n"
         "**Run:** `git status`\n"
         "\n"
         "Then check the registry for agents and report status.\n"

src/aipass/aipass/apps/modules/doctor.py

@@ -232,7 +232,7 @@ def _check_provider_manifest() -> List[CheckResult]:
     if manifest_path is None:
         results.append(
             CheckResult(
-                "hooks", GLYPH_WARN, "manifest not found", "Run setup.sh or create .claude/provider_manifest.json"
+                "hooks", GLYPH_WARN, "manifest not found", "Expected .claude/provider_manifest.json in project root"
             )
         )
         return results
@@ -270,7 +270,7 @@ def _check_provider_manifest() -> List[CheckResult]:
                 "hooks",
                 GLYPH_WARN,
                 f"{len(missing_hooks)} hook(s) missing: {', '.join(missing_hooks)}",
-                "Run setup.sh or copy from .claude/hooks/ — see .claude/hooks/README.md",
+                "Copy missing hooks to ~/.claude/hooks/ — see .claude/hooks/README.md",
             )
         )
 
@@ -294,7 +294,7 @@ def _check_provider_manifest() -> List[CheckResult]:
                     "env vars",
                     GLYPH_WARN,
                     f"{len(missing_env)} env var(s) missing: {', '.join(missing_env)}",
-                    "Run setup.sh to configure provider settings",
+                    "Add to ~/.claude/settings.json env block — see provider_manifest.json",
                 )
             )
 
@@ -329,7 +329,7 @@ def _check_provider_manifest() -> List[CheckResult]:
                     "permissions",
                     GLYPH_WARN,
                     f"{total_missing} permission rule(s) missing",
-                    "Run setup.sh to configure provider permissions",
+                    "Add to ~/.claude/settings.json permissions — see provider_manifest.json",
                 )
             )
 

src/aipass/aipass/tests/test_bootstrap.py

@@ -207,10 +207,10 @@ def test_init_project_claude_md_content(tmp_path):
     assert "## Getting Started" in content
     assert "## Available Commands" in content
     assert "## Startup Protocol" in content
-    # Startup protocol reads registry, not .trinity/
     startup_idx = content.index("## Startup Protocol")
     startup_section = content[startup_idx:]
-    assert ".trinity/" not in startup_section
+    assert ".trinity/passport.json" in startup_section
+    assert "init_report.json" in startup_section
     assert "aipass init agent" in content
     assert "ZETA_REGISTRY.json" in content