fix(cli): skills bundler resolves caller-relative paths + correct dev layout

Two correctness fixes caught during end-to-end validation:

1. Resolve skill.path relative to the file that called skills.define(),
   not the project root. The resource catalog already captures filePath
   on each SkillManifest — use it to compute the source folder.

2. In dev, copy skill bundles to {workingDir}/.trigger/skills/ (where
   the worker's cwd resolves). In deploy, keep copying to
   {outputPath}/.trigger/skills/ so the Dockerfile COPY . /app lands
   them at /app/.trigger/skills/.

Also upgrade the skill-discovery failure log from debug to warn so
config mistakes surface in the dev console instead of disappearing
silently.

Finally, update the ai-chat reference's aiChat.run() to pass chatTools
through chat.toStreamTextOptions({ tools: chatTools }) instead of
spreading them after — the auto-injected loadSkill/readFile/bash tools
would otherwise get overwritten by the explicit tools: chatTools key.

packages/cli-v3/src/build/buildWorker.ts

@@ -120,7 +120,7 @@ export async function buildWorker(options: BuildWorkerOptions) {
     });
     buildManifest = skillsResult.buildManifest;
   } catch (err) {
-    logger.debug("Skill bundling failed; continuing without skills", err);
+    logger.warn("Skill bundling failed; continuing without skills", err);
   }
 
   buildManifest = await notifyExtensionOnBuildComplete(buildContext, buildManifest);

packages/cli-v3/src/build/bundleSkills.ts

@@ -1,6 +1,6 @@
 import { createHash } from "node:crypto";
 import { readFile } from "node:fs/promises";
-import { dirname, join, resolve as resolvePath } from "node:path";
+import { dirname, isAbsolute, join, resolve as resolvePath } from "node:path";
 import type { BuildManifest, SkillManifest } from "@trigger.dev/core/v3/schemas";
 import { copyDirectoryRecursive } from "@trigger.dev/build/internal";
 import { indexWorkerManifest } from "../indexing/indexWorkerManifest.js";
@@ -60,8 +60,10 @@ export async function bundleSkills(
   } catch (err) {
     // Skill discovery via the indexer is best-effort — if the user's
     // bundle doesn't load cleanly here the downstream full indexer will
-    // surface the real error. Warn and continue with no skills.
-    logger.debug(`[bundleSkills] skill discovery failed: ${(err as Error).message}`);
+    // surface the real error. Warn so the user sees what went wrong.
+    logger.warn(
+      `[bundleSkills] skill discovery failed, skipping skill bundling: ${(err as Error).message}`
+    );
     return { buildManifest, skills: [] };
   }
 
@@ -69,10 +71,26 @@ export async function bundleSkills(
     return { buildManifest, skills: [] };
   }
 
-  const destinationRoot = join(buildManifest.outputPath, ".trigger", "skills");
+  // Destination layout differs between dev and deploy:
+  // - Dev:    the worker runs with cwd = workingDir, so skills must live at
+  //           {workingDir}/.trigger/skills/{id}/ for skill.local() to find them.
+  // - Deploy: the Dockerfile COPY picks up everything under outputPath into
+  //           /app, so we target {outputPath}/.trigger/skills/{id}/ and the
+  //           container's cwd (/app) resolves correctly.
+  const destinationRoot =
+    buildManifest.target === "dev"
+      ? join(workingDir, ".trigger", "skills")
+      : join(buildManifest.outputPath, ".trigger", "skills");
 
   for (const skill of skills) {
-    const sourcePath = resolvePath(workingDir, skill.sourcePath);
+    // Resolve the skill's source folder relative to the file that called
+    // `skills.define(...)`. Absolute paths are honored as-is.
+    const callerDir = skill.filePath
+      ? dirname(resolvePath(workingDir, skill.filePath))
+      : workingDir;
+    const sourcePath = isAbsolute(skill.sourcePath)
+      ? skill.sourcePath
+      : resolvePath(callerDir, skill.sourcePath);
     const skillMdPath = join(sourcePath, "SKILL.md");
 
     let skillMd: string;

packages/cli-v3/src/dev/devSession.ts

@@ -136,7 +136,7 @@ export async function startDevSession({
       });
       buildManifest = skillsResult.buildManifest;
     } catch (err) {
-      logger.debug("Skill bundling failed during dev rebuild", err);
+      logger.warn("Skill bundling failed during dev rebuild", err);
     }
 
     buildManifest = await notifyExtensionOnBuildComplete(buildContext, buildManifest);

references/ai-chat/src/trigger/chat.ts

@@ -495,10 +495,10 @@ export const aiChat = chat
         ...chat.toStreamTextOptions({
           registry,
           telemetry: clientData?.userId ? { userId: clientData.userId } : undefined,
+          tools: chatTools,
         }),
         model: languageModelForChatTurn(modelOverride),
         messages: messages,
-        tools: chatTools,
         stopWhen: stepCountIs(10),
         abortSignal: stopSignal,
         providerOptions: {