fix(context): merge overlay columns onto manifest columns by name (#94)

* fix(context): merge overlay columns onto manifest columns by name

composeOverlay was appending overlay columns to the manifest column list,
producing duplicate entries when dbt/metabase overlays declared a column
just to attach descriptions. The duplicates carried no `type`, so the
pydantic SourceDefinition rejected them at semantic-query time and broke
`ktx sl query` for every overlay-backed measure. Now overlay columns
match base columns by name (case-insensitive): same-name entries merge
onto the manifest (overlay fields win, type/role fall back to the base,
descriptions merge per source key) and only new names append.

* refactor(sl): split overlay columns from column_overrides and enforce TS/Python wire contract

Overlay sources now have two distinct collections: `columns:` for computed
columns (requiring `expr` + `type`) and `column_overrides:` for metadata
patches to inherited manifest columns. Composing or loading an overlay that
mixes the two — or references an unknown column — fails with a typed error.

Introduce `ResolvedSemanticLayerSource` / `resolvedSourceSchema` /
`toResolvedWire` as the strict shape sent to the Python engine, and add a
schema contract test that diffs Zod against the Pydantic JSON schema dumped
by `python -m semantic_layer dump-schema`. `SourceDefinition` is now
`extra="forbid"` on the Python side.

`loadAllSources` surfaces per-file load errors instead of swallowing them,
so validation/query paths can report manifest shard parse failures.

* fix(context): make scan description generation resilient and quiet

A transient sampleTable failure during ingest used to take out every
table in a connection: generateTableDescription returned a hardcoded
'Table not found' string into descriptions.ai, and KtxDescriptionGenerator
was constructed without a logger, so the failure left no trail anywhere.

- sampleTable / sampleColumn calls retry 3x with 200/400/800ms backoff,
  honouring KtxScanContext.signal via a new KtxAbortedError.
- On retry exhaustion or missing capability, table generation falls back
  to a metadata-only prompt built from column name / native type / comment
  / rawDescriptions. The column path follows the same rule -- call the
  LLM when any of samples or rawDescriptions are available; skip only
  when both are absent.
- Logger is now threaded from KtxScanContext into the generator. Failures
  emit structured KtxScanWarning entries (new description_fallback_used
  code, plus existing sampling_failed / enrichment_failed /
  connector_capability_missing). ktx scan groups warnings by code so a
  batch of identical failures collapses to one summary line plus sample.
- Returns null on failure instead of the 'Table not found' sentinel; the
  manifest writer's existing guard already skips empty descriptions, so
  schema YAML no longer carries misleading text. SCAN_MANAGED_DESCRIPTION_KEYS
  already strips stale 'ai' on merge, so existing YAML clears on next run.

Also suppress AI SDK v6 'system in messages' warning: pull system messages
out of KtxMessageBuilder.wrapSimple's output via a new splitKtxSystemMessages
helper and pass them top-level to generateText (preserves cacheControl
providerOptions on the SystemModelMessage). Agent-runner's local
splitSystemPromptMessages dedupes onto the shared helper.

* test(docs): align examples-docs assertions with revamped docs

PR #103 (setup/guide doc revamp) reworded several CLI examples and
connection labels; the assertions in scripts/examples-docs.test.mjs
still referenced the pre-revamp wording and were failing in CI on main.
Update the regexes to match the post-revamp content:

- drop the `--json` flag from the sl-query example expectation
- move the `Driver:` / `Status: ok` probe to the connection reference,
  which is where that output now lives (driver id is lowercase
  `postgres`, not the display name `PostgreSQL`)
- drop the obsolete `Install \`uv\`...` troubleshooting line
- accept `<connectionId>` everywhere; the docs no longer use the
  hyphenated `<connection-id>` form
- match the `warehouse` connection id used in the quickstart instead of
  the `postgres-warehouse` id only used in the README and setup ref

* fix(sl): skip TS/Python schema contract test when uv is unavailable

The TypeScript checks CI job does not install uv or Python, so the
module-level `execFileSync('uv', ...)` in schemas.contract.test.ts threw
ENOENT and failed the suite. Wrap the schema dump in a try/catch and
guard the describe block with `describe.skipIf` so the test skips in
environments without uv. Local dev and any CI job that has uv on PATH
still runs the cross-language contract assertion.

packages/llm/src/index.ts

@@ -1,6 +1,7 @@
 export { createKtxEmbeddingProvider } from './embedding-provider.js';
 export { runKtxEmbeddingHealthCheck } from './embedding-health.js';
-export { KtxMessageBuilder } from './message-builder.js';
+export { KtxMessageBuilder, splitKtxSystemMessages } from './message-builder.js';
+export type { KtxSplitSystemMessagesResult } from './message-builder.js';
 export type { KtxEmbeddingHealthCheckOptions, KtxEmbeddingHealthCheckResult } from './embedding-health.js';
 export type { KtxEmbeddingProviderDeps } from './embedding-provider.js';
 export type { KtxLlmHealthCheckDeps, KtxLlmHealthCheckOptions, KtxLlmHealthCheckResult } from './model-health.js';

packages/llm/src/message-builder.test.ts

@@ -1,6 +1,6 @@
 import type { ModelMessage } from 'ai';
 import { describe, expect, it } from 'vitest';
-import { KtxMessageBuilder } from './message-builder.js';
+import { KtxMessageBuilder, splitKtxSystemMessages } from './message-builder.js';
 import { createKtxLlmProvider } from './model-provider.js';
 
 function makeBuilder(overrides: Parameters<typeof createKtxLlmProvider>[0]['promptCaching'] = {}) {
@@ -111,3 +111,36 @@ describe('KtxMessageBuilder.build', () => {
     expect((out.tools.z as { providerOptions: any }).providerOptions.anthropic.cacheControl.ttl).toBe('5m');
   });
 });
+
+describe('splitKtxSystemMessages', () => {
+  it('returns undefined system when no system messages are present', () => {
+    const split = splitKtxSystemMessages([
+      { role: 'user', content: 'hello' },
+      { role: 'assistant', content: 'hi' },
+    ]);
+    expect(split.system).toBeUndefined();
+    expect(split.messages).toHaveLength(2);
+  });
+
+  it('returns a single system message object when one system message is present, preserving providerOptions', () => {
+    const systemMessage = {
+      role: 'system' as const,
+      content: 'You are helpful.',
+      providerOptions: { anthropic: { cacheControl: { type: 'ephemeral' } } },
+    };
+    const split = splitKtxSystemMessages([systemMessage, { role: 'user', content: 'hello' }]);
+    expect(split.system).toBe(systemMessage);
+    expect(split.messages).toEqual([{ role: 'user', content: 'hello' }]);
+  });
+
+  it('returns an array of system messages when multiple are present, in order', () => {
+    const split = splitKtxSystemMessages([
+      { role: 'system', content: 'cached' },
+      { role: 'system', content: 'fresh' },
+      { role: 'user', content: 'hello' },
+    ]);
+    expect(Array.isArray(split.system)).toBe(true);
+    expect(split.system).toHaveLength(2);
+    expect(split.messages).toEqual([{ role: 'user', content: 'hello' }]);
+  });
+});

packages/llm/src/message-builder.ts

@@ -1,7 +1,29 @@
-import type { LanguageModel, ModelMessage, ToolSet } from 'ai';
+import type { LanguageModel, ModelMessage, SystemModelMessage, ToolSet } from 'ai';
 import { isAnthropicProtocolModel } from './model-provider.js';
 import type { KtxLlmProvider, KtxPromptCacheTtl, KtxPromptParts } from './types.js';
 
+export interface KtxSplitSystemMessagesResult {
+  system: SystemModelMessage | SystemModelMessage[] | undefined;
+  messages: ModelMessage[];
+}
+
+export function splitKtxSystemMessages(messages: readonly ModelMessage[]): KtxSplitSystemMessagesResult {
+  const systemMessages: SystemModelMessage[] = [];
+  const otherMessages: ModelMessage[] = [];
+  for (const message of messages) {
+    if (message.role === 'system') {
+      systemMessages.push(message);
+    } else {
+      otherMessages.push(message);
+    }
+  }
+  return {
+    system:
+      systemMessages.length === 0 ? undefined : systemMessages.length === 1 ? systemMessages[0] : systemMessages,
+    messages: otherMessages,
+  };
+}
+
 type ToolMap = ToolSet | Record<string, Record<string, unknown>>;
 
 interface KtxMessageBuilderOptions {