cabal freeze should take current set of packages installed into account

Scenario:
1. Update list of packages in `my-package.cabal`.
2. Use `cabal install --only-dep`
3. Use `cabal configure`
4. Use `cabal build`
5. Make sure it compiles and works as expected.
6. Run `cabal freeze` to freeze this particular set of versions as working set of packages.

Expected:

In 6 `cabal freeze` freezes versions that were used during build in 5.

Current:

In 6 `cabal freeze` freezes some other set of packages somehow not exactly related to what was build.

Start by reproducing the six-step scenario using `cabal install --only-dep`, `cabal configure`, `cabal build`, and `cabal freeze`. Compare the versions frozen in step 6 with the package versions actually used during the build; done means `cabal freeze` records that working set consistently.

Written by the indexing model from the issue text.