Stale .hs files generated from .hsc files shadow non-generated .hs files

I created a minimal example at https://github.com/ntc2/cabal-hsc2hs-bug/tree/2nd-bug and have pasted the README below.

Ran into this while working around https://github.com/haskell/cabal/issues/3087.
## Problem

If you remove `Foo.hsc` and create a new `Foo.hs`, cabal continues to
use the old `Foo.hs` which it generated from the deleted `Foo.hsc`
file. To make cabal use the new `Foo.hs`, you have to delete the old,
cached `Foo.hs` from `dist/*/build`.
## Cabal and GHC versions

```
$ cabal --version
cabal-install version 1.22.6.0
using version 1.22.2.0 of the Cabal library

$ ghc --version
The Glorious Glasgow Haskell Compilation System, version 7.10.2
```
## Setup

```
$ rm -rf .cabal-sandbox
$ cabal sandbox init
```
## Source files

`bug/Main.hs`:

``` haskell
module Main where

import Foo

main = print foo
```

`bug/Foo.hsc`:

``` haskell
module Foo where

foo = "Using the old .hsc file!"
```

`new-foo/Foo.hs`

``` haskell
module Foo where

foo = "Using the new .hs file!"
```

`cabal-hsc2hs-bug.cabal`:

```
name: cabal-hsc2hs-bug
version: 0.1.0.0
license: BSD3
license-file: LICENSE
author: Nathan Collins
maintainer: nathan.collins@gmail.com
build-type: Simple
cabal-version: >=1.10

executable bug
main-is: Main.hs
other-modules: Foo
hs-source-dirs: bug
build-depends: base
default-language: Haskell2010
```
## Observed, buggy behavior

``` console
$ cabal install && .cabal-sandbox/bin/bug
[...]
"Using the old .hsc file!"
$ rm bug/Foo.hsc
$ cp new-foo/Foo.hs bug/Foo.hs
$ cabal install && .cabal-sandbox/bin/bug
[...]
"Using the old .hsc file!"
$ find dist -name 'Foo.hs' -exec rm {} \;
$ cabal install && .cabal-sandbox/bin/bug
[...]
"Using the new .hs file!"
```

Reproduce the sequence in the linked minimal example using cabal-hsc2hs-bug.cabal, bug/Foo.hsc, and new-foo/Foo.hs. Start by inspecting dist/*/build after removing Foo.hsc and adding Foo.hs. Done means cabal uses the new Foo.hs without manually deleting the cached generated file.

Written by the indexing model from the issue text.