Bump Flask to 3.1.3 in acceptance test fixtures (#4771)

## Summary
- Bump Flask from 2.2.5 to 3.1.3 in
`acceptance/bundle/environments/dependencies/`
- Bump Flask from 3.1.1 to 3.1.3 in
`acceptance/cmd/workspace/apps/run-local/app/`

Supersedes #4560 and #4578.

## Test plan
- [x] `TestAccept/bundle/environments/dependencies` passes (both
engines)
- [x] `TestAccept/cmd/workspace/apps/run-local` passes

This pull request was AI-assisted by Isaac.

Author: pietern

acceptance/bundle/environments/dependencies/requirements.txt

@@ -1 +1 @@
-Flask==2.2.5
+Flask==3.1.3

acceptance/cmd/workspace/apps/run-local/app/requirements.txt

@@ -1 +1 @@
-Flask==3.1.1
+Flask==3.1.3