haskell-language-server reports several errors and warnings

On a fresh clone of `cardano-ledger` (commit ce6f5634a9e05c933dcc62aa2a873662d4c75958), running:

```bash
nix develop
haskell-language-server
```

reports a long list of warnings and that some files failed:

```
...
Files that failed:
* /tmp/cardano-ledger/eras/allegra/impl/Setup.hs
* /tmp/cardano-ledger/eras/alonzo/impl/Setup.hs
* /tmp/cardano-ledger/eras/babbage/impl/Setup.hs
* /tmp/cardano-ledger/eras/byron/chain/executable-spec/Setup.hs
* /tmp/cardano-ledger/eras/byron/crypto/Setup.hs
* /tmp/cardano-ledger/eras/byron/crypto/test/Setup.hs
* /tmp/cardano-ledger/eras/byron/ledger/executable-spec/Setup.hs
* /tmp/cardano-ledger/eras/byron/ledger/impl/Setup.hs
* /tmp/cardano-ledger/eras/byron/ledger/impl/test/NormalFormTest.hs
* /tmp/cardano-ledger/eras/byron/ledger/impl/test/Setup.hs
* /tmp/cardano-ledger/eras/conway/impl/Setup.hs
* /tmp/cardano-ledger/eras/mary/impl/Setup.hs
* /tmp/cardano-ledger/eras/shelley/impl/Setup.hs
* /tmp/cardano-ledger/eras/shelley/test-suite/Setup.hs
* /tmp/cardano-ledger/libs/cardano-data/Setup.hs
* /tmp/cardano-ledger/libs/cardano-ledger-api/Setup.hs
* /tmp/cardano-ledger/libs/cardano-ledger-binary/Setup.hs
* /tmp/cardano-ledger/libs/cardano-ledger-conformance/Setup.hs
* /tmp/cardano-ledger/libs/cardano-ledger-test/Setup.hs
* /tmp/cardano-ledger/libs/cardano-protocol-tpraos/Setup.hs
* /tmp/cardano-ledger/libs/ledger-state/Setup.hs
* /tmp/cardano-ledger/libs/ledger-state/bench/Performance.hs
* /tmp/cardano-ledger/libs/non-integral/Setup.hs
* /tmp/cardano-ledger/libs/set-algebra/Setup.hs
* /tmp/cardano-ledger/libs/small-steps/Setup.hs
* /tmp/cardano-ledger/libs/vector-map/Setup.hs
* /tmp/cardano-ledger/scripts/cabal-targets.hs
* /tmp/cardano-ledger/scripts/check-workflow-test-matrix.hs

Completed (1094 files worked, 28 files failed)
```

See [hls.log](https://github.com/user-attachments/files/21527039/hls.log) for the full log

Reproduce the report from commit ce6f5634a9e05c933dcc62aa2a873662d4c75958 with `nix develop` followed by `haskell-language-server`. Start by reading hls.log and comparing the 28 failed files, including the various Setup.hs files and test/NormalFormTest.hs. Done means identifying the cause of the failures and confirming that the same command no longer reports those files as failed.

Written by the indexing model from the issue text.