[CI][Rebase] Fix Ready/Merge pipeline upload by stripping source_file_dependencies

Build #2233 on the vllm-omni-rebase pipeline failed both "Upload Ready
Pipeline" and "Upload Merge Pipeline" with:

  Pipeline upload rejected: `source_file_dependencies` is not a valid
  property on the `command` step.

`source_file_dependencies` is an uploader-only key understood by
upload_pipeline.py, not by Buildkite. #4478 switched the rebase pipeline's
Ready/Merge steps to raw `buildkite-agent pipeline upload` to run the full
e2e suite (bypassing diff-aware skipping), but that also bypassed the
key-stripping, so Buildkite rejected the YAML.

Add a `--all` flag to upload_pipeline.py that forces the keep-all-steps
path (changed_files=None) while still stripping source_file_dependencies,
and use it for the rebase pipeline's Ready/Merge (and Nightly) uploads.
This restores a valid upload AND retains running the full e2e suite on
main builds. Normal-CI .buildkite/pipeline.yml is unchanged (still
diff-aware).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Signed-off-by: tzhouam <tzhouam@connect.ust.hk>

.buildkite/rebase-pipeline.yaml

@@ -14,7 +14,7 @@ steps:
     depends_on: image-build
     key: upload-ready-pipeline
     commands:
-      - buildkite-agent pipeline upload .buildkite/test-ready.yml
+      - python3 .buildkite/scripts/upload_pipeline.py --upload --all .buildkite/test-ready.yml
     agents:
       queue: "cpu_queue_premerge"
 
@@ -23,7 +23,7 @@ steps:
     depends_on: image-build
     key: upload-merge-pipeline
     commands:
-      - buildkite-agent pipeline upload .buildkite/test-merge.yml
+      - python3 .buildkite/scripts/upload_pipeline.py --upload --all .buildkite/test-merge.yml
     agents:
       queue: "cpu_queue_premerge"
 
@@ -33,6 +33,6 @@ steps:
     key: upload-nightly-pipeline
     if: build.env("NIGHTLY") == "1"
     commands:
-      - buildkite-agent pipeline upload .buildkite/test-nightly.yml
+      - python3 .buildkite/scripts/upload_pipeline.py --upload --all .buildkite/test-nightly.yml
     agents:
       queue: "cpu_queue_premerge"

.buildkite/scripts/upload_pipeline.py

@@ -13,13 +13,16 @@ Test pipeline mode (e.g. test-merge.yml):
     recognize this uploader-only key).
 
 Usage:
-  python3 upload_pipeline.py [--upload] <pipeline.yml>
+  python3 upload_pipeline.py [--upload] [--all] <pipeline.yml>
 
   # Bootstrap (replaces upload_pipeline_with_skip_ci.sh):
   python3 upload_pipeline.py --upload .buildkite/pipeline.yml
 
   # Test pipeline (replaces upload_test_pipeline_with_diff_skip.py):
   python3 upload_pipeline.py --upload .buildkite/test-merge.yml
+
+  # Full suite (rebase pipeline): keep all steps, still strip the uploader-only key:
+  python3 upload_pipeline.py --upload --all .buildkite/test-merge.yml
 """
 
 from __future__ import annotations
@@ -437,11 +440,17 @@ def resolve_pipeline_path(arg: str) -> Path:
     return ROOT / path
 
 
-def render_pipeline(path: Path) -> str:
+def render_pipeline(path: Path, *, force_all: bool = False) -> str:
     text = path.read_text(encoding="utf-8")
     diff_range = resolve_diff_range()
     changed_files = resolve_changed_files()
 
+    # ``--all`` forces the keep-all-steps path (no diff-aware skipping) while still
+    # stripping ``source_file_dependencies``. Used by the rebase pipeline so main builds
+    # run the full e2e suite (see .buildkite/rebase-pipeline.yaml).
+    if force_all:
+        changed_files = None
+
     if BOOTSTRAP_MARKER in text:
         rendered = render_bootstrap_pipeline(
             text,
@@ -480,6 +489,11 @@ def main() -> int:
         action="store_true",
         help="Pipe rendered YAML to buildkite-agent pipeline upload",
     )
+    parser.add_argument(
+        "--all",
+        action="store_true",
+        help="Keep all steps (disable diff-aware skipping); still strips source_file_dependencies",
+    )
     args = parser.parse_args()
 
     path = resolve_pipeline_path(args.pipeline)
@@ -487,7 +501,7 @@ def main() -> int:
         _log(f"missing pipeline file: {path}")
         return 1
 
-    rendered = render_pipeline(path)
+    rendered = render_pipeline(path, force_all=args.all)
     if args.upload:
         upload_to_buildkite(rendered)
     else: