Fix database setup edit preservation

packages/cli/src/database-tree-picker.ts

@@ -283,10 +283,12 @@ export async function pickDatabaseScope(
       continue;
     }
 
+    const selectedNoun =
+      selectedSchemas.length === 1 ? args.schemaNoun : args.schemaNounPlural;
     const action = await args.prompts.select({
-      message: `Save ${selectedSchemas.length} ${selectedSchemas.length === 1 ? args.schemaNoun : args.schemaNounPlural} or refine tables?`,
+      message: `Enable all tables in ${selectedSchemas.length} ${selectedNoun}, or refine tables?`,
       options: [
-        { value: 'save', label: 'Save selection' },
+        { value: 'save', label: `Enable all tables in selected ${selectedNoun}` },
         { value: 'refine', label: 'Refine: choose individual tables' },
         { value: 'back', label: 'Back' },
       ],

packages/cli/src/local-adapters.test.ts

@@ -167,6 +167,40 @@ describe('CLI local ingest adapters', () => {
     ]);
   });
 
+  it('resolves BigQuery credentials_json from a file: reference for query history ingest', async () => {
+    const credentialsPath = join(tempDir, 'credentials.json');
+    await writeFile(credentialsPath, JSON.stringify({ project_id: 'demo-project' }), 'utf-8');
+    await writeProject(
+      tempDir,
+      [
+        'connections:',
+        '  bq:',
+        '    driver: bigquery',
+        '    dataset_id: analytics',
+        '    location: us',
+        `    credentials_json: 'file:${credentialsPath}'`,
+        '    historicSql:',
+        '      enabled: true',
+        '      dialect: bigquery',
+        'ingest:',
+        '  adapters:',
+        '    - historic-sql',
+        '',
+      ].join('\n'),
+    );
+    const project = await loadKtxProject({ projectDir: tempDir });
+
+    const adapters = createKtxCliLocalIngestAdapters(project, {
+      historicSqlConnectionId: 'bq',
+      sqlAnalysis: sqlAnalysisStub(),
+    });
+
+    expect(adapters.find((adapter) => adapter.source === 'historic-sql')?.skillNames).toEqual([
+      'historic_sql_table_digest',
+      'historic_sql_patterns',
+    ]);
+  });
+
   it('uses query-history wording for public BigQuery capability errors', async () => {
     await writeProject(
       tempDir,

packages/cli/src/local-adapters.ts

@@ -30,6 +30,7 @@ import {
   type ManagedPythonCoreDaemonOptions,
 } from './managed-python-http.js';
 import type { KtxOperationalLogger } from './io/logger.js';
+import { resolveKtxConfigReference } from './context/core/config-reference.js';
 
 function hasSnowflakeDriver(connection: unknown): boolean {
   return (
@@ -279,7 +280,10 @@ async function createEphemeralSnowflakeHistoricSqlClient(
 
 function bigQueryProjectId(connection: KtxBigQueryConnectionConfig, env: NodeJS.ProcessEnv): string {
   const raw = typeof connection.credentials_json === 'string' ? connection.credentials_json : '';
-  const resolved = raw.startsWith('env:') ? env[raw.slice('env:'.length)] ?? '' : raw;
+  const resolved = resolveKtxConfigReference(raw, env);
+  if (!resolved) {
+    throw new Error('Query history BigQuery connection requires credentials_json');
+  }
   const parsed = JSON.parse(resolved) as { project_id?: unknown };
   if (typeof parsed.project_id !== 'string' || parsed.project_id.trim().length === 0) {
     throw new Error('Query history BigQuery connection requires credentials_json.project_id');

packages/cli/src/setup-databases.test.ts

@@ -106,7 +106,7 @@ function makePromptAdapter(options: {
         : ['back'];
     }),
     select: vi.fn(async ({ message }) => {
-      if (message.startsWith('Save ') && message.includes(' or refine tables?')) {
+      if (message.startsWith('Enable all tables in ') && message.includes(', or refine tables?')) {
         return 'save';
       }
       if (message.includes('How much database context should KTX build?')) {
@@ -260,6 +260,48 @@ describe('setup databases step', () => {
     expect(prompts.select).toHaveBeenCalledTimes(1);
   });
 
+  it('preserves context.depth when editing an existing database connection', async () => {
+    await writeFile(
+      join(tempDir, 'ktx.yaml'),
+      [
+        'connections:',
+        '  warehouse:',
+        '    driver: sqlite',
+        '    path: ./warehouse.sqlite',
+        '    context:',
+        '      depth: deep',
+        '',
+      ].join('\n'),
+      'utf-8',
+    );
+    const prompts = makePromptAdapter({
+      selectValues: ['edit', 'warehouse', 'continue'],
+      textValues: ['./warehouse.sqlite'],
+    });
+    const testConnection = vi.fn(async () => 0);
+    const scanConnection = vi.fn(async () => 0);
+    const io = makeIo();
+    const result = await runKtxSetupDatabasesStep(
+      {
+        projectDir: tempDir,
+        inputMode: 'auto',
+        skipDatabases: false,
+        databaseSchemas: [],
+        disableQueryHistory: true,
+      },
+      io.io,
+      { prompts, testConnection, scanConnection },
+    );
+
+    expect(result.status, io.stderr()).toBe('ready');
+    const config = parseKtxProjectConfig(await readFile(join(tempDir, 'ktx.yaml'), 'utf-8'));
+    expect(config.connections.warehouse).toMatchObject({
+      driver: 'sqlite',
+      path: './warehouse.sqlite',
+      context: { depth: 'deep' },
+    });
+  });
+
   it('labels existing database connections with the database type', async () => {
     await writeFile(
       join(tempDir, 'ktx.yaml'),

packages/cli/src/setup-databases.ts

@@ -663,6 +663,12 @@ function normalizeFileReference(value: string): string {
   return `file:${normalized}`;
 }
 
+function displayFileReference(value: string | undefined): string | undefined {
+  if (value === undefined) return undefined;
+  if (value.startsWith('file:')) return value.slice('file:'.length);
+  return value;
+}
+
 function scriptedScopeConfigForDriver(
   driver: KtxSetupDatabaseDriver,
   databaseSchemas: string[],
@@ -910,7 +916,7 @@ async function buildConnectionConfig(input: {
     const credentialsPath = await promptText(
       prompts,
       'Path to service account JSON file',
-      stringConfigField(input.existingConnection, 'credentials_json'),
+      displayFileReference(stringConfigField(input.existingConnection, 'credentials_json')),
     );
     if (credentialsPath === undefined) return 'back';
     const location = await promptText(
@@ -1359,6 +1365,9 @@ function withExistingPrimaryEditPromptDefaults(input: {
   if (!Object.hasOwn(input.next, 'enabled_tables') && Array.isArray(input.previous.enabled_tables)) {
     merged.enabled_tables = input.previous.enabled_tables;
   }
+  if (!Object.hasOwn(input.next, 'context') && input.previous.context !== undefined) {
+    merged.context = input.previous.context;
+  }
   return merged;
 }