diff --git a/src/server/db/index.default-path.test.ts b/src/server/db/index.default-path.test.ts
index b9825b1..bac23b8 100644
--- a/src/server/db/index.default-path.test.ts
+++ b/src/server/db/index.default-path.test.ts
@@ -41,4 +41,18 @@ describe('sqlite default path resolution', () => {
 
     expect(sqlitePath).toBe(resolve(process.env.DATA_DIR, 'hub.db'));
   });
+
+  it('ignores the default repo DATA_DIR under vitest and still isolates sqlite', async () => {
+    process.env.DATA_DIR = './data';
+    delete process.env.DB_URL;
+    vi.resetModules();
+
+    dbModule = await import('./index.js');
+    const sqlitePath = dbModule.__dbProxyTestUtils.resolveSqlitePath();
+    const sharedRepoPath = resolve('./data/hub.db');
+
+    expect(sqlitePath).not.toBe(sharedRepoPath);
+    expect(sqlitePath).toContain(tmpdir());
+    expect(sqlitePath).toContain('metapi-vitest');
+  });
 });
diff --git a/src/server/db/index.ts b/src/server/db/index.ts
index 9c65dc5..bb27a1b 100644
--- a/src/server/db/index.ts
+++ b/src/server/db/index.ts
@@ -75,6 +75,12 @@ function isVitestRuntime(): boolean {
   return runtimeArgs.some((value) => value.includes('vitest'));
 }
 
+function isDefaultRepoDataDir(value: string | undefined): boolean {
+  const trimmed = (value || '').trim();
+  if (!trimmed) return false;
+  return resolve(trimmed) === resolve('./data');
+}
+
 function resolveVitestSqlitePath(): string | null {
   if (!isVitestRuntime()) {
     return null;
@@ -82,7 +88,7 @@ function resolveVitestSqlitePath(): string | null {
   if ((process.env.DB_URL || '').trim()) {
     return null;
   }
-  if ((process.env.DATA_DIR || '').trim()) {
+  if ((process.env.DATA_DIR || '').trim() && !isDefaultRepoDataDir(process.env.DATA_DIR)) {
     return null;
   }
 
diff --git a/src/server/db/runtimeSchemaBootstrap.test.ts b/src/server/db/runtimeSchemaBootstrap.test.ts
index d10cac9..ec31d52 100644
--- a/src/server/db/runtimeSchemaBootstrap.test.ts
+++ b/src/server/db/runtimeSchemaBootstrap.test.ts
@@ -65,6 +65,27 @@ describe('runtime schema bootstrap', () => {
     expect(executedSql.every((sqlText) => classifyLegacyCompatMutation(sqlText) === 'legacy')).toBe(true);
   });
 
+  it('tolerates non-additive live-schema drift and still emits additive runtime patch statements', () => {
+    const driftedLiveContract = __runtimeSchemaBootstrapTestUtils.cloneContract(currentContract);
+
+    delete driftedLiveContract.tables.model_availability?.columns.is_manual;
+    if (driftedLiveContract.tables.sites?.columns.status) {
+      driftedLiveContract.tables.sites.columns.status.defaultValue = null;
+    }
+    driftedLiveContract.indexes = driftedLiveContract.indexes.filter((index) => index.name !== 'accounts_site_id_idx');
+    driftedLiveContract.uniques = driftedLiveContract.uniques.filter((unique) => unique.name !== 'proxy_files_public_id_unique');
+
+    const statements = __runtimeSchemaBootstrapTestUtils.buildExternalUpgradeStatements(
+      'mysql',
+      currentContract,
+      driftedLiveContract,
+    );
+
+    expect(statements.some((sqlText) => sqlText.includes('ALTER TABLE `model_availability` ADD COLUMN `is_manual`'))).toBe(true);
+    expect(statements.some((sqlText) => sqlText.includes('CREATE INDEX `accounts_site_id_idx`'))).toBe(true);
+    expect(statements.some((sqlText) => sqlText.includes('CREATE UNIQUE INDEX `proxy_files_public_id_unique`'))).toBe(true);
+  });
+
   it('ignores duplicate mysql index and column errors when replaying additive schema statements', async () => {
     const executedSql: string[] = [];
     const duplicateColumnSql = __runtimeSchemaBootstrapTestUtils.splitSqlStatements(
diff --git a/src/server/db/runtimeSchemaBootstrap.ts b/src/server/db/runtimeSchemaBootstrap.ts
index 715ed02..1838527 100644
--- a/src/server/db/runtimeSchemaBootstrap.ts
+++ b/src/server/db/runtimeSchemaBootstrap.ts
@@ -153,6 +153,86 @@ function readSchemaContract(): SchemaContract {
   return JSON.parse(readFileSync(resolveGeneratedSchemaContractPath(), 'utf8')) as SchemaContract;
 }
 
+function cloneContract(contract: SchemaContract): SchemaContract {
+  return JSON.parse(JSON.stringify(contract)) as SchemaContract;
+}
+
+function serializeColumn(column: SchemaContract['tables'][string]['columns'][string]): string {
+  return [
+    column.logicalType,
+    column.notNull ? 'not-null' : 'nullable',
+    column.defaultValue ?? 'default:null',
+    column.primaryKey ? 'pk' : 'non-pk',
+  ].join('|');
+}
+
+function serializeIndex(index: SchemaContract['indexes'][number]): string {
+  return [index.table, index.columns.join(','), index.unique ? 'unique' : 'non-unique'].join('|');
+}
+
+function serializeUnique(unique: SchemaContract['uniques'][number]): string {
+  return [unique.table, unique.columns.join(',')].join('|');
+}
+
+function serializeForeignKey(foreignKey: SchemaContract['foreignKeys'][number]): string {
+  return [
+    foreignKey.table,
+    foreignKey.columns.join(','),
+    foreignKey.referencedTable,
+    foreignKey.referencedColumns.join(','),
+    foreignKey.onDelete ?? 'null',
+  ].join('|');
+}
+
+function buildCompatibleRuntimeBaseline(
+  currentContract: SchemaContract,
+  liveContract: SchemaContract,
+): SchemaContract {
+  const baseline: SchemaContract = {
+    tables: {},
+    indexes: [],
+    uniques: [],
+    foreignKeys: [],
+  };
+
+  for (const [tableName, liveTable] of Object.entries(liveContract.tables)) {
+    const currentTable = currentContract.tables[tableName];
+    if (!currentTable) {
+      continue;
+    }
+
+    const compatibleColumns = Object.fromEntries(
+      Object.entries(liveTable.columns)
+        .filter(([columnName, liveColumn]) => {
+          const currentColumn = currentTable.columns[columnName];
+          return currentColumn && serializeColumn(currentColumn) === serializeColumn(liveColumn);
+        }),
+    );
+
+    baseline.tables[tableName] = { columns: compatibleColumns };
+  }
+
+  const currentIndexes = new Map(currentContract.indexes.map((index) => [index.name, index]));
+  baseline.indexes = liveContract.indexes
+    .filter((index) => {
+      const currentIndex = currentIndexes.get(index.name);
+      return currentIndex && serializeIndex(currentIndex) === serializeIndex(index);
+    });
+
+  const currentUniques = new Map(currentContract.uniques.map((unique) => [unique.name, unique]));
+  baseline.uniques = liveContract.uniques
+    .filter((unique) => {
+      const currentUnique = currentUniques.get(unique.name);
+      return currentUnique && serializeUnique(currentUnique) === serializeUnique(unique);
+    });
+
+  const currentForeignKeys = new Set(currentContract.foreignKeys.map(serializeForeignKey));
+  baseline.foreignKeys = liveContract.foreignKeys
+    .filter((foreignKey) => currentForeignKeys.has(serializeForeignKey(foreignKey)));
+
+  return baseline;
+}
+
 async function createPostgresClient(connectionString: string, ssl: boolean): Promise<RuntimeSchemaClient> {
   const clientOptions: pg.ClientConfig = { connectionString };
   if (ssl) {
@@ -267,7 +347,8 @@ function buildExternalUpgradeStatements(
   currentContract: SchemaContract,
   liveContract: SchemaContract,
 ): string[] {
-  return splitSqlStatements(generateUpgradeSql(dialect, currentContract, liveContract));
+  const compatibleBaseline = buildCompatibleRuntimeBaseline(currentContract, liveContract);
+  return splitSqlStatements(generateUpgradeSql(dialect, currentContract, compatibleBaseline));
 }
 
 export async function ensureRuntimeDatabaseSchema(
@@ -300,6 +381,8 @@ export async function bootstrapRuntimeDatabaseSchema(input: RuntimeSchemaConnect
 }
 
 export const __runtimeSchemaBootstrapTestUtils = {
+  buildCompatibleRuntimeBaseline,
+  cloneContract,
   splitSqlStatements,
   buildExternalUpgradeStatements,
 };