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/context/src/sl/tools/sl-write-source.tool.ts

@@ -23,7 +23,9 @@ const slWriteSourceInputSchema = z.object({
     .describe('Name of the source to create, edit, or delete'),
   source: sourceInputSchema
     .optional()
-    .describe('Source definition (standalone with table/sql) or overlay (measures, computed columns, etc.)'),
+    .describe(
+      'Source definition (standalone with table/sql) or overlay (measures, column_overrides, computed columns, etc.)',
+    ),
   delete: z.boolean().optional().describe('Set to true to delete this source entirely'),
   rawPaths: z
     .array(z.string().min(1))
@@ -73,7 +75,8 @@ If the source already exists, this tool will overwrite it with the new definitio
 - table: For physical table/view sources (e.g., "public.orders"). Mutually exclusive with sql.
 - sql: For SQL-based sources (the SQL query). Mutually exclusive with table.
 - grain: What one row represents (e.g., ["id"], ["customer_id", "product_id"])
-- columns: All columns with type (string/number/time/boolean) and optional descriptions
+- columns: All columns with type (string/number/time/boolean) and optional descriptions. On overlays, columns are computed-only and require expr + type.
+- column_overrides: Overlay-only metadata patches for existing manifest columns (descriptions, role, visibility, constraints, enum_values, tests). Do not include type or expr.
 - joins: Relationships to other sources (to, on, relationship: many_to_one/one_to_many/one_to_one)
 - measures: Pre-defined aggregations (name, expr like "sum(amount)", optional filter, optional segments — bare names of segments defined on the same source, optional description)
 - segments: Named, reusable boolean predicates scoped to this source (name, expr — a SQL boolean over this source's columns, optional description). A measure references one with \`segments: [name]\`; a query references one with the dotted form \`source.segment_name\`. Use when the same predicate appears on 3+ measures — e.g. extract \`is_paid = true and is_refunded = '0'\` as \`segments: [{name: paid_non_refunded, expr: "..."}]\` and have each measure use \`segments: [paid_non_refunded]\` instead of re-typing the predicate inside \`sum(case when ... then x end)\`. Segments are predicates only — they cannot be selected as dimensions or grouped by; if you need to group by the predicate, add a \`columns[]\` entry instead.
@@ -113,7 +116,7 @@ Do NOT join back to a table that the SQL already aggregates from if the grain co
       try {
         await semanticLayerService.deleteSource(connectionId, sourceName, author, authorEmail);
         if (!skipIndex) {
-          const allSources = await semanticLayerService.loadAllSources(connectionId);
+          const { sources: allSources } = await semanticLayerService.loadAllSources(connectionId);
           await this.slSearchService.indexSources(connectionId, allSources).catch(() => {});
         }
         if (context.session) {
@@ -210,7 +213,7 @@ Do NOT join back to a table that the SQL already aggregates from if the grain co
       );
 
       if (!skipIndex) {
-        const allSources = await semanticLayerService.loadAllSources(connectionId);
+        const { sources: allSources } = await semanticLayerService.loadAllSources(connectionId);
         await this.slSearchService.indexSources(connectionId, allSources).catch(() => {});
       }
 
@@ -317,8 +320,9 @@ Do NOT join back to a table that the SQL already aggregates from if the grain co
       `Error: cannot write "${sourceName}" as a standalone source — a manifest entry with that name already exists.`,
       `  Writing standalone would drop the manifest's columns and joins, leaving only what you list here.`,
       `To add measures/segments on top of the manifest, rewrite this YAML as an overlay:`,
-      `  - Remove "sql:", "table:", "grain:", "columns:", and "joins:".`,
-      `  - Keep only "name:", plus "measures:", "segments:", and/or "descriptions:".`,
+      `  - Remove "sql:", "table:", "grain:", and base-table "columns:".`,
+      `  - Keep "name:" plus "measures:", "segments:", "descriptions:", "joins:", "disable_joins:",`,
+      `    "exclude_columns:", "column_overrides:", and/or computed-only "columns:" entries with expr + type.`,
       `  - The manifest's schema is inherited automatically.`,
       `If you really need a different base table, use a different source name.`,
     ].join('\n');