you need to clean your local checkout of any folders/files that have been removed from repo already:

git clean -f

That should resolve this issue.

I don't want to include this clean step in the generator because if people have local files that they are working on, I don't want to accidentally remove it.

I think we can still improve this by having the script running "git status -u" and warn users that it gonna affect fidelity of the script.

Even better, maybe script should ignore folders that are not tracked by git

Ah, "git status -u" seems a good improvement.

I'll look into that.

zmo@ is out, and this has been causing many catapult blockage ( issue 881543 ). I am taking this bug.

The following revision refers to this bug:
  https://chromium.googlesource.com/catapult/+/febcf8764dc1ab9a2b3cd87c3911c4924db45e30

commit febcf8764dc1ab9a2b3cd87c3911c4924db45e30
Author: nednguyen <nednguyen@google.com>
Date: Fri Sep 07 18:44:05 2018

Ignore files/directory that are not tracked by git when generating BUILD.gn for Telemetry

Previously, if developers working on catapult/ patches have files or directories in the
top level catapult directory that are untracked by git, generate_telemetry_build.py script
will include those files in BUILD.gn. This CL makes sure that the script
ignores those files instead.

Test: patch this CL, add random local files into catapult/,
run ./generate_telemetry_build.py --> expect that BUILD.gn doesn't change

Bug:  chromium:879554 
Change-Id: I2c05bacd09360685002273be6e8a8be5ae79c577
Reviewed-on: https://chromium-review.googlesource.com/1213349
Commit-Queue: Ned Nguyen <nednguyen@google.com>
Reviewed-by: Kenneth Russell <kbr@chromium.org>

[modify] https://crrev.com/febcf8764dc1ab9a2b3cd87c3911c4924db45e30/generate_telemetry_build.py

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/dd19a2123e6a476fb81010166b9661bfb8c74bbc

commit dd19a2123e6a476fb81010166b9661bfb8c74bbc
Author: catapult-chromium-autoroll <catapult-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Date: Fri Sep 07 21:07:52 2018

Roll src/third_party/catapult 32654a45d3da..febcf8764dc1 (6 commits)

https://chromium.googlesource.com/catapult.git/+log/32654a45d3da..febcf8764dc1


git log 32654a45d3da..febcf8764dc1 --date=short --no-merges --format='%ad %ae %s'
2018-09-07 nednguyen@google.com Ignore files/directory that are not tracked by git when generating BUILD.gn for Telemetry
2018-09-07 jbudorick@chromium.org devil: move gn files over from chromium.
2018-09-07 nastasoiuf@google.com Additional features for stacked plot
2018-09-07 simonhatch@chromium.org Dashboard - Remove TestMetadata._pre_put_hook
2018-09-07 simonhatch@chromium.org Dashboard - Remove stray print
2018-09-07 simonhatch@chromium.org Dashboard - Refactor find_anomalies to support stats later


Created with:
  gclient setdep -r src/third_party/catapult@febcf8764dc1

The AutoRoll server is located here: https://autoroll.skia.org/r/catapult-autoroll

Documentation for the AutoRoller is here:
https://skia.googlesource.com/buildbot/+/master/autoroll/README.md

If the roll is causing failures, please contact the current sheriff, who should
be CC'd on the roll, and stop the roller if necessary.

CQ_INCLUDE_TRYBOTS=luci.chromium.try:android_optional_gpu_tests_rel;luci.chromium.try:linux_optional_gpu_tests_rel;luci.chromium.try:mac_optional_gpu_tests_rel;luci.chromium.try:win_optional_gpu_tests_rel

BUG= chromium:879554 , chromium:881910 ,chromium:866423,chromium:881523
TBR=sullivan@chromium.org

Change-Id: I1f41015a567033be0e588947b705ae02435521be
Reviewed-on: https://chromium-review.googlesource.com/1213776
Reviewed-by: catapult-chromium-autoroll <catapult-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Commit-Queue: catapult-chromium-autoroll <catapult-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Cr-Commit-Position: refs/heads/master@{#589641}
[modify] https://crrev.com/dd19a2123e6a476fb81010166b9661bfb8c74bbc/DEPS