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The issue is that it expects the main-is: cabal field to be a Main module. When it isn't, we get duplicate modules. Take, for example ndmitchell/ghcid:
mgsloan@computer:~/oss/ndmitchell/ghcid$ stack ghci --test
ghcid-0.5: Test running disabled by --no-run-tests flag.
* * * * * * * *
The main module to load is ambiguous. Candidates are:
1. Package `ghcid' component exe:ghcid with main-is file: /home/mgsloan/oss/ndmitchell/ghcid/src/Ghcid.hs
2. Package `ghcid' component test:ghcid_test with main-is file: /home/mgsloan/oss/ndmitchell/ghcid/src/Test.hs
You can specify which one to pick by:
* Specifying targets to stack ghci e.g. stack ghci ghcid:exe:ghcid
* Specifying what the main is e.g. stack ghci --main-is ghcid:exe:ghcid
* Choosing from the candidate above [1..2]
* * * * * * * *
Specify main module to use (press enter to load none): 1
Loading main module from cadidate 1, --main-is /home/mgsloan/oss/ndmitchell/ghcid/src/Ghcid.hs
The following GHC options are incompatible with GHCi and have not been passed to it: -threaded
Configuring GHCi with the following packages: ghcid
GHCi, version 7.10.2: http://www.haskell.org/ghc/ :? for help
unknown option: 'c'
<no location info>:
module ‘main@main:Ghcid’ is defined in multiple files: /home/mgsloan/oss/ndmitchell/ghcid/src/Ghcid.hs
/home/mgsloan/oss/ndmitchell/ghcid/src/Ghcid.hs
Failed, modules loaded: none.
<no location info>:
Could not find module ‘Ghcid’
It is not a module in the current program, or in any known package.