In case you want to move non-pipeline files out first, I think it seems more reasonable to delete all pipelines first so that we don't have to update those dead code.

The following revision refers to this bug:
  https://chromium.googlesource.com/infra/infra/+/4bf2069ffa994419debd1a360b12b654508eb658

commit 4bf2069ffa994419debd1a360b12b654508eb658
Author: Jeffrey Li <lijeffrey@chromium.org>
Date: Thu May 17 19:57:17 2018

[Findit] Flake Analyzer - Moving modules under waterfall/flake to servicess/flake_failure

No functional changes.
Moving most non-pipelines under waterfall/flake to services/flake_failure.

Bug: 843810
Change-Id: I9447eb066a6b1bbd3939a2ee24059f4c5f91d59f
Reviewed-on: https://chromium-review.googlesource.com/1063312
Commit-Queue: Jeffrey Li <lijeffrey@chromium.org>
Reviewed-by: Shuotao Gao <stgao@chromium.org>

[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/culprit_util.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/handlers/process_flake_analysis_request.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/confidence_score_util.py
[rename] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/model/flake/test/triggering_sources_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/culprit_util_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/next_commit_position_utils.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/waterfall/flake/initialize_flake_pipeline.py
[rename] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/flake_constants.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/test/event_reporting_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/flake_analysis_util.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/lookback_algorithm_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/run_swarming_util.py
[delete] https://crrev.com/f7465c9c4693b44883452a2a4624d6abf552d70e/appengine/findit/waterfall/flake/test/lookback_algorithm_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/waterfall/flake/trigger_flake_analyses_pipeline.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/waterfall/flake/test/flake_analysis_service_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/pass_rate_util_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/pipelines/flake_failure/update_monorail_bug_pipeline.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/pipelines/flake_failure/get_isolate_sha_pipeline.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/confidence_score_util_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/issue_tracking_service.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/swarmbot_util.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/pass_rate_util.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/heuristic_analysis.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/event_reporting.py
[rename] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/confidence.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/data_point_util.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/findit_api.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/test/issue_tracking_service_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/handlers/flake/check_flake.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/test/findit_api_test.py
[rename] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/model/flake/triggering_sources.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/pipelines/flake_failure/create_bug_for_flake_pipeline.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/flake_try_job.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/flake_analysis_util_test.py
[delete] https://crrev.com/f7465c9c4693b44883452a2a4624d6abf552d70e/appengine/findit/waterfall/flake/lookback_algorithm.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/flake_try_job_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/data_point_util_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/pipelines/flake_failure/test/determine_approximate_pass_rate_pipeline_test.py
[rename] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/services/flake_failure/test/confidence_test.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/model/base_swarming_task.py
[modify] https://crrev.com/4bf2069ffa994419debd1a360b12b654508eb658/appengine/findit/waterfall/flake/flake_analysis_util.py