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If keeping the intermediate files then don't have clean remove them?
# To make stack.yaml or cabal.project and no other, mark the file we copy from
# as intermediate. This is all we want when not doing a GHC upgrade.
#
# Comment out these .INTERMEDIATE targets to allow these files to be kept.
# .INTERMEDIATE: ghc-$(GHC_VERSION).$(CABAL_VIA).project
# .INTERMEDIATE: ghc-$(GHC_UPGRADE).$(CABAL_VIA).project
# .INTERMEDIATE: ghc-$(GHC_VERSION).$(STACK_VIA).yaml
# .INTERMEDIATE: ghc-$(GHC_UPGRADE).$(STACK_VIA).yaml
.INTERMEDIATE: ghc-$(GHC_VERSION).sha256map.nix
.INTERMEDIATE: ghc-$(GHC_UPGRADE).sha256map.nix$ make -f project-files.mk clean
updo/project-dhall/Makefile:51: warning: overriding recipe for target 'ghc-9.0.2.dhall2stack.yaml'
updo/project-dhall/Makefile:44: warning: ignoring old recipe for target 'ghc-9.0.2.dhall2stack.yaml'
updo/project-dhall/Makefile:66: warning: overriding recipe for target 'ghc-9.0.2.dhall2cabal.project'
updo/project-dhall/Makefile:58: warning: ignoring old recipe for target 'ghc-9.0.2.dhall2cabal.project'
updo/project-dhall2config/Makefile:80: warning: overriding recipe for target 'ghc-9.0.2.dhall2config.project'
updo/project-dhall2config/Makefile:69: warning: ignoring old recipe for target 'ghc-9.0.2.dhall2config.project'
rm -f ghc-*.stack.* ghc-*.dhall2config.* ghc-*.dhall2cabal.* ghc-*.dhall2stack.* ghc-*.stack2cabal.* ghc-*.cabal2stack.* ghc-*.dhall2yaml2stack.* ghc-*.sha256map.nix
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