I've looked deeper:

(1) This gc runs inside builder's checkout, not the git cache. So, git cache is WAI: https://cs.chromium.org/chromium/tools/depot_tools/git_cache.py?dr&l=311

(2) We don't want (1) to happen anyway, so perhaps we should run the same command in the checkout.

CL attempting to disable gc/autopacking: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/973900 

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/tools/depot_tools/+/b3065fb6a19f946287d64e234c761ee223ab13f5

commit b3065fb6a19f946287d64e234c761ee223ab13f5
Author: Andrii Shyshkalov <tandrii@chromium.org>
Date: Wed Mar 21 20:24:26 2018

bot_update: don't repack, don't gc in main repo of builder's checkout.

The main purpose is to avoid running slow and useless operation in
chromium/src checkouts. Ideally, this should be done in every DEPS-ed
repo, too, but that requires substantially more changes in gclient.
Thus, this CL provides biggest bang for the buck.

Example led build: https://ci.chromium.org/swarming/task/3c62efb31ed3a910?server=chromium-swarm.appspot.com

R=hinoka@chromium.org

Bug:  822437 
Change-Id: I347d85e5cb5158b77969a755b67ca2289fb39d40
Reviewed-on: https://chromium-review.googlesource.com/973900
Commit-Queue: Andrii Shyshkalov <tandrii@chromium.org>
Reviewed-by: Ryan Tseng <hinoka@chromium.org>

[modify] https://crrev.com/b3065fb6a19f946287d64e234c761ee223ab13f5/recipes/recipe_modules/bot_update/resources/bot_update.py

This should be fixed. +tikuta@ FYI.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/0a5dd12a54ee50fdca40c2e7265ba9cc63c78f78

commit 0a5dd12a54ee50fdca40c2e7265ba9cc63c78f78
Author: depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com <depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Date: Wed Mar 21 21:53:23 2018

Roll src/third_party/depot_tools/ a68d82cb2..b3065fb6a (1 commit)

https://chromium.googlesource.com/chromium/tools/depot_tools.git/+log/a68d82cb2fde..b3065fb6a19f

$ git log a68d82cb2..b3065fb6a --date=short --no-merges --format='%ad %ae %s'
2018-03-21 tandrii bot_update: don't repack, don't gc in main repo of builder's checkout.

Created with:
  roll-dep src/third_party/depot_tools
BUG= chromium:822437 


The AutoRoll server is located here: https://depot-tools-chromium-roll.skia.org

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.


TBR=agable@chromium.org

Change-Id: I51da70698709b41506098aa74e59301efe3a85a2
Reviewed-on: https://chromium-review.googlesource.com/974126
Commit-Queue: depot-tools-chromium-autoroll <depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Reviewed-by: depot-tools-chromium-autoroll <depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Cr-Commit-Position: refs/heads/master@{#544860}
[modify] https://crrev.com/0a5dd12a54ee50fdca40c2e7265ba9cc63c78f78/DEPS

It didn't really help, see [1] for full log:



===Running git config gc.autodetach 0 ===
In directory: /b/s/w/ir/cache/builder/src
===Succeeded in 0.0 mins of git config gc.autodetach 0 ===
===Running git config gc.autopacklimit 0 ===
In directory: /b/s/w/ir/cache/builder/src
===Succeeded in 0.0 mins of git config gc.autopacklimit 0 ===
===Running git remote set-url origin /b/s/w/ir/cache/git/chromium.googlesource.com-chromium-src ===
In directory: /b/s/w/ir/cache/builder/src
===Succeeded in 0.0 mins of git remote set-url origin /b/s/w/ir/cache/git/chromium.googlesource.com-chromium-src ===
......
===Applying gerrit ref===
Repo is 'https://chromium.googlesource.com/chromium/src' @ 'cd3021a5d555d1d49e7df2bd789c269ada30354a', ref is 'refs/changes/88/1042888/6', root is 'src'
===Running git reset --hard ===
In directory: src
HEAD is now at cd3021a5d555 Improved export to Linux test.
===Succeeded in 0.2 mins of git reset --hard ===
===Running git fetch https://chromium.googlesource.com/chromium/src refs/changes/88/1042888/6 ===
In directory: src
From https://chromium.googlesource.com/a/chromium/src
 * branch                      refs/changes/88/1042888/6 -> FETCH_HEAD
Auto packing the repository for optimum performance.
See "git help gc" for manual housekeeping.



Let's do more drastic option: according to https://git-scm.com/docs/git-gc
gc.auto = 0
disables all GC. Let's try that.



[1] https://logs.chromium.org/v/?s=chromium%2Fbuildbucket%2Fcr-buildbucket.appspot.com%2F8947426792478842352%2F%2B%2Fsteps%2Fbot_update%2F0%2Fstdout

https://chromium-review.googlesource.com/#/c/chromium/tools/depot_tools/+/1045491

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/tools/depot_tools/+/5e5f2d60353bb93898302458f37ae667d60c7b8e

commit 5e5f2d60353bb93898302458f37ae667d60c7b8e
Author: Andrii Shyshkalov <tandrii@chromium.org>
Date: Sat May 05 01:44:46 2018

bot_update: attempt to disable GC completely on main repo.

Motivation: see  https://crbug.com/822437#c6 
tl;dr apparently, auotpacking still happens, this CL tries to stop
prevent it harder than before.

R=vadimsh@chromium.org

Bug:  822437 
Change-Id: Idda384bdebd96c10ac79c48b0622f84550060362
Reviewed-on: https://chromium-review.googlesource.com/1045491
Reviewed-by: Vadim Shtayura <vadimsh@chromium.org>
Commit-Queue: Andrii Shyshkalov <tandrii@chromium.org>

[modify] https://crrev.com/5e5f2d60353bb93898302458f37ae667d60c7b8e/recipes/recipe_modules/bot_update/resources/bot_update.py

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/f72b55ae7689aad347728d0bff4517d486c885b5

commit f72b55ae7689aad347728d0bff4517d486c885b5
Author: depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com <depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Date: Sat May 05 05:56:05 2018

Roll src/third_party/depot_tools/ ea240053f..5e5f2d603 (1 commit)

https://chromium.googlesource.com/chromium/tools/depot_tools.git/+log/ea240053f956..5e5f2d60353b

$ git log ea240053f..5e5f2d603 --date=short --no-merges --format='%ad %ae %s'
2018-05-04 tandrii bot_update: attempt to disable GC completely on main repo.

Created with:
  roll-dep src/third_party/depot_tools
BUG= chromium:822437 


The AutoRoll server is located here: https://depot-tools-chromium-roll.skia.org

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.


TBR=agable@chromium.org

Change-Id: I9587aced9d864d929fca9566a0a6df34db52fa09
Reviewed-on: https://chromium-review.googlesource.com/1045888
Commit-Queue: depot-tools-chromium-autoroll <depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Reviewed-by: depot-tools-chromium-autoroll <depot-tools-chromium-autoroll@skia-buildbots.google.com.iam.gserviceaccount.com>
Cr-Commit-Position: refs/heads/master@{#556308}
[modify] https://crrev.com/f72b55ae7689aad347728d0bff4517d486c885b5/DEPS