feat(MULTIVERSION-0001): wire trueref.json into pipeline + per-version rules

- Add migration 0003: recreate repository_configs with nullable version_id
  column and two partial unique indexes (repo-wide: version_id IS NULL,
  per-version: (repository_id, version_id) WHERE version_id IS NOT NULL)
- Update schema.ts to reflect the new composite structure with uniqueIndex
  partial constraints via drizzle-orm sql helper
- IndexingPipeline: parse trueref.json / context7.json after crawl, apply
  excludeFiles filter before diff computation, update totalFiles accordingly
- IndexingPipeline: persist repo-wide rules (version_id=null) and
  version-specific rules (when versionId set) via upsertRepoConfig helper
- Add matchesExcludePattern static helper supporting plain filename,
  glob prefix (docs/legacy*), and exact path patterns
- context endpoint: split getRules into repo-wide + version-specific lookup
  with dedup merge; pass versionId at call site
- Update test DB loaders to include migration 0003
- Add pipeline tests for excludeFiles, repo-wide rules persistence, and
  per-version rules persistence
- Add integration tests for merged rules, repo-only rules, and dedup logic

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

src/lib/server/db/migrations/0003_multiversion_config.sql

@@ -0,0 +1,30 @@
+PRAGMA foreign_keys=OFF;
+--> statement-breakpoint
+CREATE TABLE `__new_repository_configs` (
+	`repository_id` text NOT NULL,
+	`version_id` text,
+	`project_title` text,
+	`description` text,
+	`folders` text,
+	`exclude_folders` text,
+	`exclude_files` text,
+	`rules` text,
+	`previous_versions` text,
+	`updated_at` integer NOT NULL,
+	FOREIGN KEY (`repository_id`) REFERENCES `repositories`(`id`) ON UPDATE no action ON DELETE cascade
+);
+--> statement-breakpoint
+INSERT INTO `__new_repository_configs`
+  (repository_id, version_id, project_title, description, folders, exclude_folders, exclude_files, rules, previous_versions, updated_at)
+  SELECT repository_id, NULL, project_title, description, folders, exclude_folders, exclude_files, rules, previous_versions, updated_at
+  FROM `repository_configs`;
+--> statement-breakpoint
+DROP TABLE `repository_configs`;
+--> statement-breakpoint
+ALTER TABLE `__new_repository_configs` RENAME TO `repository_configs`;
+--> statement-breakpoint
+PRAGMA foreign_keys=ON;
+--> statement-breakpoint
+CREATE UNIQUE INDEX `uniq_repo_config_base` ON `repository_configs` (`repository_id`) WHERE `version_id` IS NULL;
+--> statement-breakpoint
+CREATE UNIQUE INDEX `uniq_repo_config_version` ON `repository_configs` (`repository_id`, `version_id`) WHERE `version_id` IS NOT NULL;

src/lib/server/db/migrations/meta/_journal.json

@@ -22,6 +22,13 @@
 			"when": 1774461897742,
 			"tag": "0002_silky_stellaris",
 			"breakpoints": true
+		},
+		{
+			"idx": 3,
+			"version": "6",
+			"when": 1743155877000,
+			"tag": "0003_multiversion_config",
+			"breakpoints": true
 		}
 	]
 }

src/lib/server/db/schema.ts

@@ -1,4 +1,13 @@
-import { blob, integer, primaryKey, real, sqliteTable, text } from 'drizzle-orm/sqlite-core';
+import { sql } from 'drizzle-orm';
+import {
+	blob,
+	integer,
+	primaryKey,
+	real,
+	sqliteTable,
+	text,
+	uniqueIndex
+} from 'drizzle-orm/sqlite-core';
 
 // ---------------------------------------------------------------------------
 // repositories
@@ -148,21 +157,33 @@ export const indexingJobs = sqliteTable('indexing_jobs', {
 // ---------------------------------------------------------------------------
 // repository_configs
 // ---------------------------------------------------------------------------
-export const repositoryConfigs = sqliteTable('repository_configs', {
-	repositoryId: text('repository_id')
-		.primaryKey()
-		.references(() => repositories.id, { onDelete: 'cascade' }),
-	projectTitle: text('project_title'),
-	description: text('description'),
-	folders: text('folders', { mode: 'json' }).$type<string[]>(),
-	excludeFolders: text('exclude_folders', { mode: 'json' }).$type<string[]>(),
-	excludeFiles: text('exclude_files', { mode: 'json' }).$type<string[]>(),
-	rules: text('rules', { mode: 'json' }).$type<string[]>(),
-	previousVersions: text('previous_versions', { mode: 'json' }).$type<
-		{ tag: string; title: string; commitHash?: string }[]
-	>(),
-	updatedAt: integer('updated_at', { mode: 'timestamp' }).notNull()
-});
+export const repositoryConfigs = sqliteTable(
+	'repository_configs',
+	{
+		repositoryId: text('repository_id')
+			.notNull()
+			.references(() => repositories.id, { onDelete: 'cascade' }),
+		versionId: text('version_id'),
+		projectTitle: text('project_title'),
+		description: text('description'),
+		folders: text('folders', { mode: 'json' }).$type<string[]>(),
+		excludeFolders: text('exclude_folders', { mode: 'json' }).$type<string[]>(),
+		excludeFiles: text('exclude_files', { mode: 'json' }).$type<string[]>(),
+		rules: text('rules', { mode: 'json' }).$type<string[]>(),
+		previousVersions: text('previous_versions', { mode: 'json' }).$type<
+			{ tag: string; title: string; commitHash?: string }[]
+		>(),
+		updatedAt: integer('updated_at', { mode: 'timestamp' }).notNull()
+	},
+	(table) => [
+		uniqueIndex('uniq_repo_config_base')
+			.on(table.repositoryId)
+			.where(sql`${table.versionId} IS NULL`),
+		uniqueIndex('uniq_repo_config_version')
+			.on(table.repositoryId, table.versionId)
+			.where(sql`${table.versionId} IS NOT NULL`)
+	]
+);
 
 // ---------------------------------------------------------------------------
 // settings