Remove "This is taking a long time" progress timeout and TimeoutConfiguration.

This reverts commit 76cbc462.

There have been some more additional reports of a missing 'package:characters' import after upgrading flutter, as well as problems with detecting the correct language version. This has me concerned that our pub caching logic is incorrect. Instead of the tool attempting to guess when pub should be run, always delegate to pub.

Integration tests must only go through the real file system/process manager/platform. The global indirection makes this code harder to understand than if it directly referred to the concrete instances that are being used.

Update the integration shard to use a const instance of a LocalFIleSystem, LocalProcessManager, and LocalPlatform. Remove global usage and apply testWithoutContext.