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;