fix(build): warn before --no-incremental wipes embeddings (#986)

* fix(build): warn before --no-incremental wipes embeddings

A full rebuild (either via --no-incremental or when promoted by an engine/
schema/version mismatch) silently drops every row from the embeddings
table. Users who just spent minutes generating embeddings lose them with
no warning, and subsequent \`codegraph search\` returns zero hits with no
indication why.

Add a warnOnEmbeddingsWipe step to setupPipeline that runs after the
incremental/forceFullRebuild decision is made. When the build will be
full AND the embeddings table is non-empty, log:

  Full rebuild will discard N embeddings; re-run \`codegraph embed\`
  after the build.

The warning sits at the pipeline entry, so it fires uniformly for the
native orchestrator and the JS fallback path. It is silent when the
embeddings table is missing, empty, or when the build is incremental.

Closes #982

* fix(build): re-check embeddings on native-orchestrator version mismatch (#986)

The catch block that handles native-orchestrator throws performs a late
promotion to a full rebuild when the codegraph_version mismatch is
detected. warnOnEmbeddingsWipe already ran in setupPipeline before
forceFullRebuild was set here, so this path previously wiped embeddings
silently — exactly the scenario the initial guard was meant to close.

Call warnOnEmbeddingsWipe again after setting ctx.forceFullRebuild = true
so the late-promotion path surfaces the same warning as the other full
rebuild paths.

Impact: 1 functions changed, 6 affected

Author: carlos-alm

src/domain/graph/builder/pipeline.ts

@@ -106,6 +106,21 @@ function checkEngineSchemaMismatch(ctx: PipelineContext): void {
   }
 }
 
+function warnOnEmbeddingsWipe(ctx: PipelineContext): void {
+  const willBeFullBuild = !ctx.incremental || ctx.forceFullRebuild;
+  if (!willBeFullBuild) return;
+  let count = 0;
+  try {
+    count = (ctx.db.prepare('SELECT COUNT(*) AS c FROM embeddings').get() as { c: number }).c;
+  } catch {
+    return; // embeddings table missing — nothing to warn about
+  }
+  if (count === 0) return;
+  warn(
+    `Full rebuild will discard ${count} embedding${count === 1 ? '' : 's'}; re-run \`codegraph embed\` after the build.`,
+  );
+}
+
 function loadAliases(ctx: PipelineContext): void {
   ctx.aliases = loadPathAliases(ctx.rootDir);
   if (ctx.config.aliases) {
@@ -151,6 +166,7 @@ function setupPipeline(ctx: PipelineContext): void {
 
   initializeEngine(ctx);
   checkEngineSchemaMismatch(ctx);
+  warnOnEmbeddingsWipe(ctx);
   loadAliases(ctx);
 
   // Workspace packages (monorepo)
@@ -960,6 +976,10 @@ export async function buildGraph(
             `Codegraph version changed (${prevVersion} → ${CODEGRAPH_VERSION}), promoting to full rebuild.`,
           );
           ctx.forceFullRebuild = true;
+          // Re-check embeddings: the initial warnOnEmbeddingsWipe ran before
+          // forceFullRebuild was set here, so the silent-data-loss guard
+          // would otherwise miss this late-promotion path (#986 follow-up).
+          warnOnEmbeddingsWipe(ctx);
         }
       }
     }