Make e2e tests slightly more explicit and consistent.

[BillyONeal]

• Get rid of e2e-ports/overlays and just hoist the contents up to e2e-ports directly.
• Get rid of e2e-ports/overlay-triplets and hoist that directory to a peer of e2e-ports. (triplets are not ports and should not be in a directory named ports)
• Stop adding e2e-ports/overlays as an overlay-ports flag in front of all tests. This causes 'spooky action at a distance' where it's harder to review what a test is testing for as what the test actually depends on was not named in the test.
• Where possible, use --x-builtin-ports-root rather than --overlay-ports. I believe it would be good to break any dependency on a "real" vcpkg-root to run e2e tests, but several tests need e.g. vcpkg-cmake and vcpkg-cmake-config to exist, so I've left that as outside the scope of this change.

Drive-by change:

• Add -StartAt to end-to-end-tests.ps1 to help when making changes like this to avoid N^2 runs :)

[BillyONeal]

(I wrote this because I was going to add more tests and realized given the wide number of places ports could be added that I was not myself sure where it should be added)