Merge remote-tracking branch 'public-gh/master' into paperclip-routines

* public-gh/master: (46 commits)
  chore(lockfile): refresh pnpm-lock.yaml (#1377)
  fix: manage codex home per company by default
  Ensure agent home directories exist before use
  Handle directory entries in imported zip archives
  Fix portability import and org chart test blockers
  Fix PR verify failures after merge
  fix: address greptile follow-up feedback
  Address remaining Greptile portability feedback
  docs: clarify quickstart npx usage
  Add guarded dev restart handling
  Fix PAP-576 settings toggles and transcript default
  Add username log censor setting
  fix: use standard toggle component for permission controls
  fix: add missing setPrincipalPermission mock in portability tests
  fix: use fixed 1280x640 dimensions for org chart export image
  Adjust default CEO onboarding task copy
  fix: link Agent Company to agentcompanies.io in export README
  fix: strip agents and projects sections from COMPANY.md export body
  fix: default company export page to README.md instead of first file
  Add default agent instructions bundle
  ...

# Conflicts:
#	packages/adapters/pi-local/src/server/execute.ts
#	packages/db/src/migrations/meta/0039_snapshot.json
#	packages/db/src/migrations/meta/_journal.json
#	server/src/__tests__/agent-permissions-routes.test.ts
#	server/src/__tests__/agent-skills-routes.test.ts
#	server/src/services/company-portability.ts
#	skills/paperclip/references/company-skills.md
#	ui/src/api/agents.ts

packages/db/src/migrations/0030_friendly_loners.sql

@@ -1,43 +0,0 @@
-DO $$
-BEGIN
-	IF NOT EXISTS (
-		SELECT 1
-		FROM information_schema.tables
-		WHERE table_schema = 'public' AND table_name = 'company_skills'
-	) THEN
-		CREATE TABLE "company_skills" (
-			"id" uuid PRIMARY KEY DEFAULT gen_random_uuid() NOT NULL,
-			"company_id" uuid NOT NULL,
-			"slug" text NOT NULL,
-			"name" text NOT NULL,
-			"description" text,
-			"markdown" text NOT NULL,
-			"source_type" text DEFAULT 'local_path' NOT NULL,
-			"source_locator" text,
-			"source_ref" text,
-			"trust_level" text DEFAULT 'markdown_only' NOT NULL,
-			"compatibility" text DEFAULT 'compatible' NOT NULL,
-			"file_inventory" jsonb DEFAULT '[]'::jsonb NOT NULL,
-			"metadata" jsonb,
-			"created_at" timestamp with time zone DEFAULT now() NOT NULL,
-			"updated_at" timestamp with time zone DEFAULT now() NOT NULL
-		);
-	END IF;
-END $$;
---> statement-breakpoint
-DO $$
-BEGIN
-	IF NOT EXISTS (
-		SELECT 1
-		FROM pg_constraint
-		WHERE conname = 'company_skills_company_id_companies_id_fk'
-	) THEN
-		ALTER TABLE "company_skills"
-		ADD CONSTRAINT "company_skills_company_id_companies_id_fk"
-		FOREIGN KEY ("company_id") REFERENCES "public"."companies"("id")
-		ON DELETE no action ON UPDATE no action;
-	END IF;
-END $$;
---> statement-breakpoint
-CREATE UNIQUE INDEX IF NOT EXISTS "company_skills_company_slug_idx" ON "company_skills" USING btree ("company_id","slug");--> statement-breakpoint
-CREATE INDEX IF NOT EXISTS "company_skills_company_name_idx" ON "company_skills" USING btree ("company_id","name");

packages/db/src/migrations/0035_colorful_rhino.sql

@@ -1,27 +0,0 @@
-ALTER TABLE "company_skills" ADD COLUMN "key" text;--> statement-breakpoint
-UPDATE "company_skills"
-SET "key" = CASE
-  WHEN COALESCE("metadata"->>'sourceKind', '') = 'paperclip_bundled' THEN 'paperclipai/paperclip/' || "slug"
-  WHEN (COALESCE("metadata"->>'sourceKind', '') = 'github' OR "source_type" = 'github')
-    AND COALESCE("metadata"->>'owner', '') <> ''
-    AND COALESCE("metadata"->>'repo', '') <> ''
-    THEN lower("metadata"->>'owner') || '/' || lower("metadata"->>'repo') || '/' || "slug"
-  WHEN COALESCE("metadata"->>'sourceKind', '') = 'managed_local' THEN 'company/' || "company_id"::text || '/' || "slug"
-  WHEN (COALESCE("metadata"->>'sourceKind', '') = 'url' OR "source_type" = 'url')
-    THEN 'url/'
-      || COALESCE(
-        NULLIF(regexp_replace(lower(regexp_replace(COALESCE("source_locator", ''), '^https?://([^/]+).*$','\1')), '[^a-z0-9._-]+', '-', 'g'), ''),
-        'unknown'
-      )
-      || '/'
-      || substr(md5(COALESCE("source_locator", "slug")), 1, 10)
-      || '/'
-      || "slug"
-  WHEN "source_type" = 'local_path' AND COALESCE("source_locator", '') <> ''
-    THEN 'local/' || substr(md5("source_locator"), 1, 10) || '/' || "slug"
-  ELSE 'company/' || "company_id"::text || '/' || "slug"
-END
-WHERE "key" IS NULL;--> statement-breakpoint
-ALTER TABLE "company_skills" ALTER COLUMN "key" SET NOT NULL;--> statement-breakpoint
-DROP INDEX IF EXISTS "company_skills_company_slug_idx";--> statement-breakpoint
-CREATE UNIQUE INDEX "company_skills_company_key_idx" ON "company_skills" USING btree ("company_id","key");

packages/db/src/migrations/0039_curly_maria_hill.sql

@@ -0,0 +1 @@
+ALTER TABLE "instance_settings" ADD COLUMN "general" jsonb DEFAULT '{}'::jsonb NOT NULL;

packages/db/src/migrations/0040_spotty_the_renegades.sql

@@ -0,0 +1,22 @@
+CREATE TABLE "company_skills" (
+	"id" uuid PRIMARY KEY DEFAULT gen_random_uuid() NOT NULL,
+	"company_id" uuid NOT NULL,
+	"key" text NOT NULL,
+	"slug" text NOT NULL,
+	"name" text NOT NULL,
+	"description" text,
+	"markdown" text NOT NULL,
+	"source_type" text DEFAULT 'local_path' NOT NULL,
+	"source_locator" text,
+	"source_ref" text,
+	"trust_level" text DEFAULT 'markdown_only' NOT NULL,
+	"compatibility" text DEFAULT 'compatible' NOT NULL,
+	"file_inventory" jsonb DEFAULT '[]'::jsonb NOT NULL,
+	"metadata" jsonb,
+	"created_at" timestamp with time zone DEFAULT now() NOT NULL,
+	"updated_at" timestamp with time zone DEFAULT now() NOT NULL
+);
+--> statement-breakpoint
+ALTER TABLE "company_skills" ADD CONSTRAINT "company_skills_company_id_companies_id_fk" FOREIGN KEY ("company_id") REFERENCES "public"."companies"("id") ON DELETE no action ON UPDATE no action;--> statement-breakpoint
+CREATE UNIQUE INDEX "company_skills_company_key_idx" ON "company_skills" USING btree ("company_id","key");--> statement-breakpoint
+CREATE INDEX "company_skills_company_name_idx" ON "company_skills" USING btree ("company_id","name");

packages/db/src/migrations/meta/0041_snapshot.json

@@ -1,6 +1,6 @@
 {
   "id": "c49c6ac1-3acd-4a7b-91e5-5ad193b154a5",
-  "prevId": "70a51031-63ca-4491-8794-54cae9e07c66",
+  "prevId": "ff2d3ea8-018e-44ec-9e7d-dfa81b2ef772",
   "version": "7",
   "dialect": "postgresql",
   "tables": {
@@ -11390,4 +11390,4 @@
     "schemas": {},
     "tables": {}
   }
-}
+}

packages/db/src/migrations/meta/_journal.json

@@ -292,9 +292,23 @@
     {
       "idx": 41,
       "version": "7",
+      "when": 1774011294562,
+      "tag": "0039_curly_maria_hill",
+      "breakpoints": true
+    },
+    {
+      "idx": 42,
+      "version": "7",
+      "when": 1774031825634,
+      "tag": "0040_spotty_the_renegades",
+      "breakpoints": true
+    },
+    {
+      "idx": 43,
+      "version": "7",
       "when": 1774008910991,
       "tag": "0041_reflective_captain_universe",
       "breakpoints": true
     }
   ]
-}
+}

packages/db/src/schema/instance_settings.ts

@@ -5,6 +5,7 @@ export const instanceSettings = pgTable(
   {
     id: uuid("id").primaryKey().defaultRandom(),
     singletonKey: text("singleton_key").notNull().default("default"),
+    general: jsonb("general").$type<Record<string, unknown>>().notNull().default({}),
     experimental: jsonb("experimental").$type<Record<string, unknown>>().notNull().default({}),
     createdAt: timestamp("created_at", { withTimezone: true }).notNull().defaultNow(),
     updatedAt: timestamp("updated_at", { withTimezone: true }).notNull().defaultNow(),