From 4ea2cb8ddd18ca78a91d799885f3ff8806fc8425 Mon Sep 17 00:00:00 2001
From: Ilya Baryshnikov <zlonast3@gmail.com>
Date: Mon, 24 Aug 2026 15:23:04 +0300
Subject: [PATCH 1/3] add test

---
 .../ConditionalFlagOverride/cabal.out              |  8 ++++++++
 .../ConditionalFlagOverride/cabal.project          |  8 ++++++++
 .../ConditionalFlagOverride/cabal.test.hs          |  4 ++++
 .../ConditionalFlagOverride/test.cabal             | 14 ++++++++++++++
 4 files changed, 34 insertions(+)
 create mode 100644 cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.out
 create mode 100644 cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.project
 create mode 100644 cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.test.hs
 create mode 100644 cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/test.cabal

diff --git a/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.out b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.out
new file mode 100644
index 00000000000..b9929ed847c
--- /dev/null
+++ b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.out
@@ -0,0 +1,8 @@
+# cabal build
+Resolving dependencies...
+Build profile: -w ghc-<GHCVER> -O1
+In order, the following will be built:
+ - test-0.1 (lib) (first run)
+Configuring library for test-0.1...
+Preprocessing library for test-0.1...
+Building library for test-0.1...
diff --git a/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.project b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.project
new file mode 100644
index 00000000000..46c1945879c
--- /dev/null
+++ b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.project
@@ -0,0 +1,8 @@
+packages: .
+
+if impl(ghc >= 9.0)
+  package test
+    flags: +bar
+
+package test
+  flags: -bar
diff --git a/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.test.hs b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.test.hs
new file mode 100644
index 00000000000..db6203e6546
--- /dev/null
+++ b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/cabal.test.hs
@@ -0,0 +1,4 @@
+import Test.Cabal.Prelude
+
+main = cabalTest $ do
+  cabal "build" []
diff --git a/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/test.cabal b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/test.cabal
new file mode 100644
index 00000000000..e34eb303670
--- /dev/null
+++ b/cabal-testsuite/PackageTests/ProjectConfig/ConditionalFlagOverride/test.cabal
@@ -0,0 +1,14 @@
+cabal-version:  3.0
+name:           test
+version:        0.1
+license:        BSD-3-Clause
+build-type:     Simple
+
+flag bar
+  default: True
+  manual: True
+
+library
+  default-language: Haskell2010
+  if flag(bar)
+    buildable: False

From 357d0fb2fee26b1c5a6b3110badcb1f7bf5ab607 Mon Sep 17 00:00:00 2001
From: Ilya Baryshnikov <zlonast3@gmail.com>
Date: Mon, 24 Aug 2026 15:23:24 +0300
Subject: [PATCH 2/3] reverse order

---
 cabal-install/src/Distribution/Client/ProjectConfig/Legacy.hs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cabal-install/src/Distribution/Client/ProjectConfig/Legacy.hs b/cabal-install/src/Distribution/Client/ProjectConfig/Legacy.hs
index a733d61fe4a..22a88019540 100644
--- a/cabal-install/src/Distribution/Client/ProjectConfig/Legacy.hs
+++ b/cabal-install/src/Distribution/Client/ProjectConfig/Legacy.hs
@@ -227,7 +227,7 @@ instantiateProjectConfigSkeletonWithCompiler os arch impl _flags skel = go $ map
     go :: CondTree FlagName ([(Maybe URI, ProjectConfigPath)], ProjectConfig) -> ProjectConfig
     go (CondNode (_, l) ts) =
       let branches = concatMap processBranch ts
-       in l <> mconcat branches
+       in mconcat branches <> l
     processBranch (CondBranch cnd t mf) = case cnd of
       (Lit True) -> [go t]
       (Lit False) -> maybe [] ((: []) . go) mf

From faebf6b4b6feca06cad83fbea9e594bb87c98b24 Mon Sep 17 00:00:00 2001
From: Ilya Baryshnikov <zlonast3@gmail.com>
Date: Mon, 24 Aug 2026 15:24:19 +0300
Subject: [PATCH 3/3] add changelog

---
 changelog.d/12279.md | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 changelog.d/12279.md

diff --git a/changelog.d/12279.md b/changelog.d/12279.md
new file mode 100644
index 00000000000..72888a64efb
--- /dev/null
+++ b/changelog.d/12279.md
@@ -0,0 +1,28 @@
+---
+synopsis: Unconditional project settings now override settings in conditional clauses
+packages: [cabal-install]
+prs: 12279
+issues: 9293
+---
+
+Fix a bug where an unconditional setting in a project file (e.g.
+`cabal.project` or an imported file such as `cabal.project.local`) was silently
+ignored when an earlier setting for the same option appeared inside a
+conditional clause.
+
+Previously the conditional clauses were always merged _after_ the unconditional
+fields, so a conditional won regardless of where it appeared in the file:
+
+```cabal
+if impl(ghc >= 9.0)
+  package foo
+    flags: +bar
+
+package foo
+  flags: -bar
+```
+
+This would build `foo` with `bar` enabled, because `+bar` was applied last.
+The skeleton is now combined in the opposite order, applying the unconditional
+fields last so they take precedence over the conditional ones. Overrides in
+`cabal.project.local` are therefore no longer shadowed by conditionals.