Conditionally built module are not loaded if Cabal disables them and stack.yaml reenables them with stack (revisit after commercialhaskell/stack#5480)

### Summary
If some modules are conditionally built depending on flags, and the flag is off by default, then even if one explicitly enable that flag in corresponding `stack.yaml` used by HLS, those modules are not loaded automatically.

### Your environment
Output of `haskell-language-server --probe-tools` or `haskell-language-server-wrapper --probe-tools`:

```sh
$ ~/Library/Application\ Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-wrapper-0.8.0-darwin --probe-tools
haskell-language-server version: 0.8.0.0 (GHC: 8.10.1) (PATH: /Users/hiromi/Library/Application Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-wrapper-0.8.0-darwin) (GIT hash: eb58f13f7b8e4f9bc771af30ff9fd82dc4309ff5)
Tool versions found on the $PATH
cabal: 3.2.0.0
stack: 2.5.1
ghc: 8.6.5
```

Which lsp-client do you use: VSCode

Describe your project (alternative: link to the project): I have the [repro repo](/konn/hls-conditional-modules) for this.

The project has the following module hierarchy:

```
src
├── Lib
│ └── Internal.hs
├── Lib.hs
├── Lib2
│ └── Internal.hs
└── Lib2.hs
```

Here, `Lib` imports `Lib.Internal` and `Lib2` imports `Lib2.Internal`.
`Lib2` and `Lib2.Internal` are conditionally built based on the flag `dsiable-lib2`, which is on by default in `cabal` file.
In `stack.yaml`, which is used for both building and HLS, `disable-lib2` flag is explicitly disabled as follows, hence `Lib2*` must be built with stack:

```yaml
flags:
hls-conditional-modules:
disable-lib2: false
```

Contents of `hie.yaml`:
Not needed; but I have one with generated by `gen-hie`:
```yaml
cradle:
stack:
- path: "src"
component: "hls-conditional-modules:lib"
```

### Steps to reproduce
1. Open project directory, without any file open.
2. Open `src/Lib2.hs`
3. Wait for modules to be loaded

### Expected behaviour
Lib2 will be successfully loaded without any error.

### Actual behaviour
HLS could not load `Lib2.Internal`:

```json
{
"resource": "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/src/Lib2.hs",
"owner": "Haskell (hls-conditional-modules)",
"severity": 8,
"message": "Could not load module ‘Lib2.Internal’\nIt is a member of the hidden package ‘hls-conditional-modules-0.1.0.0’.\nYou can run ‘:set -package hls-conditional-modules’ to expose it.\n(Note: this unloads all the modules in the current scope.)",
"source": "not found",
"startLineNumber": 3,
"startColumn": 8,
"endLineNumber": 3,
"endColumn": 21
}
```

If one opens `src/Lib2/Internal.hs`, the above error dissapears.
Additionally, If one disables `disable-lib2` flag in Cabal file, `Lib2.Internal` will be loaded just by opening `Lib2.hs` alone.

### Include debug information
Execute in the root of your project the command `haskell-language-server --debug .` and paste the logs here:

Debug output:

```
$ ~/Library/Application\ Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-wrapper-0.8.0-darwin --debug
Found "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/hie.yaml" for "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/a"
Module "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/a" is loaded by Cradle: Cradle {cradleRootDir = "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules", cradleOptsProg = CradleAction: Stack}
Run entered for haskell-language-server-wrapper(haskell-language-server-wrapper-0.8.0-darwin) Version 0.8.0.0, Git revision eb58f13f7b8e4f9bc771af30ff9fd82dc4309ff5 (dirty) x86_64 ghc-8.10.1
Current directory: /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules
Operating system: darwin
Arguments: ["--debug"]
Cradle directory: /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules
Cradle type: Stack

Tool versions found on the $PATH
cabal: 3.2.0.0
stack: 2.5.1
ghc: 8.6.5

Consulting the cradle to get project GHC version...
Project GHC version: 8.10.3
haskell-language-server exe candidates: ["haskell-language-server-8.10.3","haskell-language-server-8.10","haskell-language-server"]
Cannot find any haskell-language-server exe, looked for: haskell-language-server-8.10.3, haskell-language-server-8.10, haskell-language-server
金 01 29 hiromi@Swing ~/Documents/Programming/Haskell/git/hls-conditional-modules
$ ~/Library/Application\ Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-0.8.0-darwin-8.10.3 --debug
haskell-language-server version: 0.8.0.0 (GHC: 8.10.3) (PATH: /Users/hiromi/Library/Application Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-0.8.0-darwin-8.10.3) (GIT hash: eb58f13f7b8e4f9bc771af30ff9fd82dc4309ff5)
(haskell-language-server)Ghcide setup tester in /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules.
Report bugs at https://github.com/haskell/haskell-language-server/issues

Tool versions found on the $PATH
cabal: 3.2.0.0
stack: 2.5.1
ghc: 8.6.5

Step 1/4: Finding files to test in /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules
Found 5 files

Step 2/4: Looking for hie.yaml files that control setup
Found 1 cradle

Step 3/4: Initializing the IDE

Step 4/4: Type checking the files
[INFO] Consulting the cradle for "src/Lib/Internal.hs"
Output from setting up the cradle Cradle {cradleRootDir = "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules", cradleOptsProg = CradleAction: Stack}
> hls-conditional-modules> configure (lib)
> Configuring hls-conditional-modules-0.1.0.0...
> hls-conditional-modules> initial-build-steps (lib)
> Configuring GHCi with the following packages: hls-conditional-modules
> /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/.stack-work/install/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/snapshots/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/programs/x86_64-osx/ghc-8.10.3/lib/ghc-8.10.3/package.conf.d
[INFO] Using interface files cache dir: ghcide
[INFO] Making new HscEnv[main]
[INFO] Consulting the cradle for "src/Lib2.hs"
Output from setting up the cradle Cradle {cradleRootDir = "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules", cradleOptsProg = CradleAction: Stack}
> hls-conditional-modules> configure (lib)
> Configuring hls-conditional-modules-0.1.0.0...
> hls-conditional-modules> initial-build-steps (lib)
> Configuring GHCi with the following packages: hls-conditional-modules
> /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/.stack-work/install/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/snapshots/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/programs/x86_64-osx/ghc-8.10.3/lib/ghc-8.10.3/package.conf.d
[INFO] Using interface files cache dir: ghcide
[INFO] Using interface files cache dir: ghcide
[INFO] Making new HscEnv[main,main]
[INFO] Consulting the cradle for "src/Lib2/Internal.hs"
Output from setting up the cradle Cradle {cradleRootDir = "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules", cradleOptsProg = CradleAction: Stack}
> hls-conditional-modules> configure (lib)
> Configuring hls-conditional-modules-0.1.0.0...
> hls-conditional-modules> initial-build-steps (lib)
> Configuring GHCi with the following packages: hls-conditional-modules
> /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/.stack-work/install/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/snapshots/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/programs/x86_64-osx/ghc-8.10.3/lib/ghc-8.10.3/package.conf.d
[INFO] Using interface files cache dir: ghcide
[INFO] Using interface files cache dir: ghcide
[INFO] Using interface files cache dir: ghcide
[INFO] Making new HscEnv[main,main,main]
[INFO] Consulting the cradle for "Setup.hs"
Output from setting up the cradle Cradle {cradleRootDir = "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules", cradleOptsProg = CradleAction: Stack}
File: /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/Setup.hs
Hidden: no
Range: 1:1-2:1
Source: cradle
Severity: DsError
Message:
Multi Cradle: No prefixes matched
pwd: /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules
filepath: /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/Setup.hs
prefixes:
("src",Stack {component = Just "hls-conditional-modules:lib", stackYaml = Nothing})
Files that failed:
[INFO] finish: User TypeCheck (took 0.06s)
* /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/Setup.hs
```

Paste the logs from the lsp-client, e.g. for [VS Code](https://github.com/haskell/vscode-haskell#troubleshooting)

LSP logs:

```
[client] run command: "/Users/hiromi/Library/Application Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-0.8.0-darwin-8.10.3 --lsp"
[client] debug command: "/Users/hiromi/Library/Application Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-0.8.0-darwin-8.10.3 --lsp"
[client] server cwd: undefined
haskell-language-server version: 0.8.0.0 (GHC: 8.10.3) (PATH: /Users/hiromi/Library/Application Support/Code/User/globalStorage/haskell.haskell/haskell-language-server-0.8.0-darwin-8.10.3) (GIT hash: eb58f13f7b8e4f9bc771af30ff9fd82dc4309ff5)
Starting (haskell-language-server)LSP server...
with arguments: LspArguments {argLSP = True, argsCwd = Nothing, argFiles = [], argsShakeProfiling = Nothing, argsTesting = False, argsExamplePlugin = False, argsDebugOn = False, argsLogFile = Nothing, argsThreads = 0, argsProjectGhcVersion = False}
with plugins: [PluginId "brittany",PluginId "class",PluginId "eval",PluginId "floskell",PluginId "fourmolu",PluginId "ghcide",PluginId "hlint",PluginId "importLens",PluginId "moduleName",PluginId "ormolu",PluginId "pragmas",PluginId "retrie",PluginId "stylish-haskell",PluginId "tactic"]
in directory: /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules
If you are seeing this in a terminal, you probably should have run ghcide WITHOUT the --lsp option!
Started LSP server in 0.00s
2021-01-29 11:52:18.469968 [ThreadId 25] - Registering ide configuration: IdeConfiguration {workspaceFolders = fromList [NormalizedUri 326243741438682258 "file:///Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules"], clientSettings = hashed Nothing}
2021-01-29 11:52:18.471264 [ThreadId 25] - Configuration changed: Object (fromList [("haskell",Object (fromList [("hlint",Object (fromList [("logLevel",String "info"),("executablePath",String "/Users/hiromi/.local/bin/hlint")])),("logFile",String ""),("updateBehavior",String "keep-up-to-date"),("hlintOn",Bool True),("formatOnImportOn",Bool True),("indentationRules",Object (fromList [("enabled",Bool True)])),("liquidOn",Bool False),("languageServerVariant",String "haskell-language-server"),("serverExecutablePath",String ""),("diagnosticsOnChange",Bool True),("completionSnippetsOn",Bool True),("maxNumberOfProblems",Number 100.0),("formattingProvider",String "fourmolu"),("trace",Object (fromList [("server",String "off")]))]))])
2021-01-29 11:52:18.471905 [ThreadId 25] - Opened text document: file:///Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/src/Lib2.hs
2021-01-29 11:52:18.472613 [ThreadId 105] - hlint:getIdeas:file:NormalizedFilePath "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/src/Lib2.hs"
2021-01-29 11:52:18.47305 [ThreadId 109] - Consulting the cradle for "src/Lib2.hs"
Output from setting up the cradle Cradle {cradleRootDir = "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules", cradleOptsProg = CradleAction: Stack}
2021-01-29 11:52:18.730881 [ThreadId 127] - Plugin.makeCodeLens (ideLogger)
> hls-conditional-modules> configure (lib)
> Configuring hls-conditional-modules-0.1.0.0...
> hls-conditional-modules> initial-build-steps (lib)
> Configuring GHCi with the following packages: hls-conditional-modules
> /Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/.stack-work/install/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/snapshots/x86_64-osx/9a76837884c2ac46e9c194c478c3b6e3b88485dcc802a09c5f1784038d24c283/8.10.3/pkgdb:/Users/hiromi/.stack/programs/x86_64-osx/ghc-8.10.3/lib/ghc-8.10.3/package.conf.d
2021-01-29 11:52:22.260249 [ThreadId 109] - Using interface files cache dir: ghcide
2021-01-29 11:52:22.260319 [ThreadId 109] - Making new HscEnv[main]
2021-01-29 11:52:22.273968 [ThreadId 199] - hlint:getIdeas:file:NormalizedFilePath "/Users/hiromi/Documents/Programming/Haskell/git/hls-conditional-modules/src/Lib2.hs"
2021-01-29 11:52:22.27579 [ThreadId 254] - finish: getSession (took 0.00s)
2021-01-29 11:52:22.278784 [ThreadId 350] - finish: codeLens (took 0.00s)
2021-01-29 11:52:22.27927 [ThreadId 364] - finish: (took 0.00s)
2021-01-29 11:52:22.279577 [ThreadId 367] - finish: ModuleName.ghcSession (took 0.00s)
2021-01-29 11:52:22.280069 [ThreadId 372] - finish: ModuleName.GetParsedModule (took 0.00s)
2021-01-29 11:52:57.777813 [ThreadId 433] - finish: CodeAction (took 0.00s)
2021-01-29 11:52:58.002377 [ThreadId 439] - finish: CodeAction:PackageExports (took 0.22s)
2021-01-29 11:52:58.002629 [ThreadId 440] - finish: importLens (took 0.00s)
2021-01-29 11:52:58.002753 [ThreadId 442] - finish: MinimalImports (took 0.00s)
2021-01-29 11:52:58.003021 [ThreadId 444] - finish: addPragma (took 0.00s)
2021-01-29 11:52:58.003235 [ThreadId 446] - finish: retrie (took 0.00s)
2021-01-29 11:52:58.003459 [ThreadId 448] - finish: tactic (took 0.00s)
2021-01-29 11:52:58.564398 [ThreadId 453] - Plugin.makeCodeLens (ideLogger)
2021-01-29 11:52:58.564829 [ThreadId 454] - finish: getSession (took 0.00s)
2021-01-29 11:52:58.565176 [ThreadId 456] - finish: codeLens (took 0.00s)
2021-01-29 11:52:58.565468 [ThreadId 458] - finish: (took 0.00s)
2021-01-29 11:52:58.565849 [ThreadId 460] - finish: ModuleName.ghcSession (took 0.00s)
2021-01-29 11:52:58.566617 [ThreadId 462] - finish: ModuleName.GetParsedModule (took 0.00s)
2021-01-29 11:56:42.555448 [ThreadId 468] - finish: CodeAction (took 0.00s)
2021-01-29 11:56:42.555638 [ThreadId 470] - finish: CodeAction:PackageExports (took 0.00s)
2021-01-29 11:56:42.555941 [ThreadId 472] - finish: importLens (took 0.00s)
2021-01-29 11:56:42.556063 [ThreadId 474] - finish: MinimalImports (took 0.00s)
2021-01-29 11:56:42.55655 [ThreadId 476] - finish: addPragma (took 0.00s)
2021-01-29 11:56:42.556789 [ThreadId 478] - finish: retrie (took 0.00s)
2021-01-29 11:56:42.557005 [ThreadId 480] - finish: tactic (took 0.00s)
```

Start with the linked repro project and compare the Cabal conditional flag with the stack.yaml override and hie.yaml cradle. Reproduce the failure by opening src/Lib2.hs before src/Lib2/Internal.hs, and review commercialhaskell/stack#5480 first because the issue requests revisiting this after that work; done means Lib2 loads without manually opening its internal module.

Written by the indexing model from the issue text.