fix(api): propagate lenient structural-validation flag to batch + pipeline

Main already reuses the per-modality input handlers in batch and pipeline
(#244), so the modality-aware reuse from the video QA sweep was redundant.
Port only the remaining unique piece: pass lenient: skipStructuralValidation
to the handler so batched/pipelined PDF tools that opt out of structural
validation behave like the single-file factory path. Keeps main's safer
explicit image-decode chain (HEIC/RAW/SVG/autoOrient) and AI fileId threading.

apps/api/src/routes/batch.ts

@@ -249,6 +249,7 @@ export async function registerBatchRoutes(app: FastifyInstance): Promise<void> {
               processFilename,
               {
                 scratchDir: batchScratch,
+                lenient: getToolConfig(toolId)?.skipStructuralValidation,
               },
             );
             processBuffer = prepared.buffer;

apps/api/src/routes/pipeline.ts

@@ -304,6 +304,7 @@ export async function registerPipelineRoutes(app: FastifyInstance): Promise<void
       try {
         const prepared = await inputHandlerFor(inputModality).prepare(fileBuffer, filename, {
           scratchDir: pipelineScratch,
+          lenient: getToolConfig(firstToolId ?? "")?.skipStructuralValidation,
         });
         fileBuffer = prepared.buffer;
         filename = prepared.filename;
@@ -893,7 +894,10 @@ export async function registerPipelineRoutes(app: FastifyInstance): Promise<void
           const prepared = await inputHandlerFor(batchModality).prepare(
             processBuffer,
             processFilename,
-            { scratchDir: pipelineBatchScratch },
+            {
+              scratchDir: pipelineBatchScratch,
+              lenient: getToolConfig(pipeline.steps[0]?.toolId ?? "")?.skipStructuralValidation,
+            },
           );
           processBuffer = prepared.buffer;
           processFilename = prepared.filename;