refactor: adopt toolkit DatabaseLayer across ep-cli, ep-admin, and MCP server

Replace manual createDatabase() + createXyzRepository() + addFinalizer()
boilerplate with toolkit's EffectPatternRepositoryService,
ApplicationPatternRepositoryService, and new SkillRepositoryService.

- Add SkillRepositoryService + SkillRepositoryLive to toolkit
- Update DatabaseLayer to include all 3 repository services
- Migrate 5 ep-admin command files (search, lock, install, show, skills)
- Migrate ep-cli pattern-repo-commands and install service
- Delete unused ep-cli utils/database.ts helper
- Fix helpers.test.ts to match REQUIRED_TABLES after jobs removal
- Update DATABASE_ARCHITECTURE.md for v0.12.3 stats

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: PaulJPhilp

docs/DATABASE_ARCHITECTURE.md

@@ -298,14 +298,21 @@ These files enumerate columns explicitly in raw SQL INSERT statements. They don'
 
 ## Current State
 
-As of v0.12.1 (2026-02-11):
+As of v0.12.3 (2026-02-11):
 
 | Table | Row count | Notes |
 |---|---|---|
-| `effect_patterns` | 309 | All linked to `application_patterns`, all have `rule` |
+| `effect_patterns` | 304 | All linked to `application_patterns`, all have `rule` and `summary` |
 | `application_patterns` | 16 | 16 top-level categories |
-| `pattern_relations` | 455 | Populated from MDX `related:` frontmatter |
+| `pattern_relations` | 445 | Populated from MDX `related:` frontmatter |
 | `skills` | 16 | One per application pattern category |
 | `skill_patterns` | 309 | All patterns assigned to a skill |
 
 All 5 tables are actively populated. The `jobs` and `pattern_jobs` tables were removed in migration 0004.
+
+### v0.12.3 changes
+
+- Deleted 5 duplicate patterns (`data-chunk`, `data-duration`, `observability-custom-metrics`, `observability-tracing-spans`, `leverage-structured-logging`) — row count dropped from 309 to 304
+- All 77 schema patterns now have `summary` populated from frontmatter (previously extracted from body at sync time)
+- 4 core-concepts patterns renamed to disambiguate duplicate titles
+- `pattern_relations` rebuilt with updated `related:` slugs (445 rows, down from 455 due to removed patterns)

packages/ep-admin/src/install-commands.ts

@@ -1,13 +1,14 @@
 /**
  * Install and rules commands for AI tool integration
- * 
+ *
  * Commands for installing Effect patterns into AI tools and generating skills
  */
 
 import {
-	createApplicationPatternRepository,
-	createDatabase,
-	createEffectPatternRepository,
+	ApplicationPatternRepositoryService,
+	DatabaseLayer,
+	EffectPatternRepositoryLive,
+	EffectPatternRepositoryService,
 	type SkillLevel,
 } from "@effect-patterns/toolkit";
 import { Command, Options } from "@effect/cli";
@@ -162,18 +163,7 @@ export const installAddCommand = Command.make("add", {
 						return yield* Effect.fail(new Error(`Unsupported tool: ${tool}`));
 					}
 
-					const conn = yield* Effect.try({
-						try: () => createDatabase(),
-						catch: (error) =>
-							new Error(
-								`Failed to create database connection: ${error instanceof Error ? error.message : String(error)}`
-							),
-					});
-					yield* Effect.addFinalizer(() =>
-						Effect.promise(() => conn.close())
-					);
-
-					const repo = createEffectPatternRepository(conn.db);
+					const repo = yield* EffectPatternRepositoryService;
 					const searchParams: {
 						query?: string;
 						skillLevel?: SkillLevel;
@@ -287,6 +277,8 @@ Your AI tool configuration has been updated with Effect patterns!`,
 						{ type: "success" }
 					);
 				})
+			).pipe(
+				Effect.provide(EffectPatternRepositoryLive),
 			) as any
 	)
 );
@@ -415,10 +407,8 @@ export const installSkillsCommand = Command.make("skills", {
 				colorize("\n🎓 Generating Skills from Effect Patterns\n", "BRIGHT")
 			);
 
-			const conn = createDatabase();
-			yield* Effect.addFinalizer(() => Effect.promise(() => conn.close()));
-			const apRepo = createApplicationPatternRepository(conn.db);
-			const epRepo = createEffectPatternRepository(conn.db);
+			const epRepo = yield* EffectPatternRepositoryService;
+			const apRepo = yield* ApplicationPatternRepositoryService;
 
 			yield* Console.log(
 				colorize("📖 Loading patterns from database...", "CYAN")
@@ -681,7 +671,9 @@ export const installSkillsCommand = Command.make("skills", {
 				"✨ Skills Generation Complete!",
 				{ type: "success" }
 			);
-		})) as any;
+		})).pipe(
+			Effect.provide(DatabaseLayer),
+		) as any;
 	})
 );
 

packages/ep-admin/src/lock-commands.ts

@@ -5,9 +5,9 @@
  */
 
 import {
-    createApplicationPatternRepository,
-    createDatabase,
-    createEffectPatternRepository,
+    ApplicationPatternRepositoryService,
+    DatabaseLayer,
+    EffectPatternRepositoryService,
 } from "@effect-patterns/toolkit";
 import { Args, Command, Options } from "@effect/cli";
 import { Effect } from "effect";
@@ -89,16 +89,20 @@ const performEntityOperation = (
 	});
 
 /**
- * Get repository for entity type
+ * Get repository for entity type from pre-constructed services
  */
-const getRepository = (db: any, entityType: string): Repository | null => {
+const getRepository = (
+	epRepo: Repository,
+	apRepo: Repository,
+	entityType: string
+): Repository | null => {
 	switch (entityType) {
 		case "pattern":
 		case "effect-pattern":
-			return createEffectPatternRepository(db);
+			return epRepo;
 		case "application-pattern":
 		case "ap":
-			return createApplicationPatternRepository(db);
+			return apRepo;
 		default:
 			return null;
 	}
@@ -130,17 +134,11 @@ export const handleEntityOperation = (
 ) =>
 	Effect.scoped(
 		Effect.gen(function* () {
-			const db = yield* Effect.try({
-				try: () => createDatabase(),
-				catch: (error) =>
-					new Error(
-						`Failed to create database connection: ${error instanceof Error ? error.message : String(error)}`
-					),
-			});
-			yield* Effect.addFinalizer(() => Effect.promise(() => db.close()));
+			const epRepo = yield* EffectPatternRepositoryService;
+			const apRepo = yield* ApplicationPatternRepositoryService;
 
 			const entityType = options.type.toLowerCase();
-			const repo = getRepository(db.db, entityType);
+			const repo = getRepository(epRepo, apRepo, entityType);
 
 			if (!repo) {
 				yield* Display.showError(
@@ -163,6 +161,7 @@ export const handleEntityOperation = (
 			yield* Display.showSuccess(`${entityName} has been ${actionText}`);
 		})
 	).pipe(
+		Effect.provide(DatabaseLayer),
 		Effect.catchAll((error) =>
 			Effect.gen(function* () {
 				yield* Display.showError(

packages/ep-admin/src/search-commands.ts

@@ -3,8 +3,8 @@
  */
 
 import {
-	createDatabase,
-	createEffectPatternRepository,
+	EffectPatternRepositoryLive,
+	EffectPatternRepositoryService,
 } from "@effect-patterns/toolkit";
 import { Args, Command } from "@effect/cli";
 import { Console, Effect } from "effect";
@@ -28,18 +28,7 @@ export const searchCommand = Command.make("search", {
 						`\n🔍 Searching for patterns matching "${args.query}"...\n`
 					);
 
-					const db = yield* Effect.try({
-						try: () => createDatabase(),
-						catch: (error) =>
-							new Error(
-								`Failed to create database connection: ${error instanceof Error ? error.message : String(error)}`
-							),
-					});
-					yield* Effect.addFinalizer(() =>
-						Effect.promise(() => db.close())
-					);
-
-					const repo = createEffectPatternRepository(db.db);
+					const repo = yield* EffectPatternRepositoryService;
 					const dbPatterns = yield* Effect.tryPromise({
 						try: () =>
 							repo.search({
@@ -106,6 +95,7 @@ export const searchCommand = Command.make("search", {
 					}
 				})
 			).pipe(
+				Effect.provide(EffectPatternRepositoryLive),
 				Effect.catchAll((error) =>
 					Effect.gen(function* () {
 						yield* Display.showError(

packages/ep-admin/src/services/db/__tests__/helpers.test.ts

@@ -20,8 +20,6 @@ describe("Database Service Helpers", () => {
 			expect(REQUIRED_TABLES).toEqual([
 				"application_patterns",
 				"effect_patterns",
-				"jobs",
-				"pattern_jobs",
 				"pattern_relations",
 			]);
 		});