diff --git a/doc/manual/rl-next/include-rearrangement.md b/doc/manual/rl-next/include-rearrangement.md
new file mode 100644
index 000000000..370c40450
--- /dev/null
+++ b/doc/manual/rl-next/include-rearrangement.md
@@ -0,0 +1,20 @@
+---
+synopsis: "Includes are now qualified with library name"
+category: Development
+cls: [2178]
+credits: jade
+---
+
+The Lix includes have all been rearranged to be of the form `"lix/libexpr/foo.hh"` instead of `"foo.hh"`.
+This was already supported externally for a migration period, but it is now being applied to all the internal usages within Lix itself.
+The goal of this change is to both clarify where a file is from and to avoid polluting global include paths with things like `config.h` that might conflict with other projects.
+
+For other details, see the release notes of Lix 2.90.0, under "Rename all the libraries" in Breaking Changes.
+
+To fix an external project with sources in `src` which has a separate build directory (such that headers are in `../src` relative to where the compiler is running):
+
+```
+lix_root=$HOME/lix
+(cd $lix_root && nix develop -c 'meson setup build && ninja -C build subprojects/lix-clang-tidy/liblix-clang-tidy.so')
+run-clang-tidy -checks='-*,lix-fixincludes' -load=$lix_root/build/subprojects/lix-clang-tidy/liblix-clang-tidy.so -p build/ -header-filter '\.\./src/.*\.h' -fix src
+```
diff --git a/src/include/lix b/src/include/lix
new file mode 120000
index 000000000..a96aa0ea9
--- /dev/null
+++ b/src/include/lix
@@ -0,0 +1 @@
+..
\ No newline at end of file
diff --git a/src/libcmd/meson.build b/src/libcmd/meson.build
index 82071b3b2..dd66cf3fa 100644
--- a/src/libcmd/meson.build
+++ b/src/libcmd/meson.build
@@ -53,6 +53,8 @@ libcmd = library(
     nlohmann_json,
     liblix_doc,
   ],
+  # '../include' for self references like "lix/libcmd/*.hh"
+  include_directories : [ '../include' ],
   cpp_pch : cpp_pch,
   install : true,
   # FIXME(Qyriad): is this right?
@@ -69,7 +71,8 @@ custom_target(
 )
 
 liblixcmd = declare_dependency(
-  include_directories : '.',
+  # FIXME(jade): remove old '.' include directory
+  include_directories : include_directories('.', '../include'),
   link_with : libcmd,
 )
 
diff --git a/src/libexpr/meson.build b/src/libexpr/meson.build
index 02a335cbd..3efdca022 100644
--- a/src/libexpr/meson.build
+++ b/src/libexpr/meson.build
@@ -278,6 +278,7 @@ libexpr = library(
   ],
   # for shared.hh
   include_directories : [
+    '../',
     '../libmain',
   ],
   cpp_pch : cpp_pch,
@@ -293,7 +294,8 @@ install_headers(
 )
 
 liblixexpr = declare_dependency(
-  include_directories : include_directories('.'),
+  # FIXME(jade): remove old '.' include directory
+  include_directories : include_directories('.', '../include'),
   sources : libexpr_settings_header,
   link_with : libexpr,
 )
@@ -301,7 +303,7 @@ liblixexpr = declare_dependency(
 # FIXME: remove when https://git.lix.systems/lix-project/lix/issues/359 is fixed.
 if is_static
   liblixexpr_mstatic = declare_dependency(
-    include_directories : include_directories('.'),
+    include_directories : include_directories('.', '../include'),
     sources : libexpr_settings_header,
     link_whole : libexpr,
   )
diff --git a/src/libfetchers/meson.build b/src/libfetchers/meson.build
index e388e5498..3d06eebd4 100644
--- a/src/libfetchers/meson.build
+++ b/src/libfetchers/meson.build
@@ -55,6 +55,7 @@ libfetchers = library(
     liblixutil,
     nlohmann_json,
   ],
+  include_directories : [ '../include' ],
   cpp_pch : cpp_pch,
   install : true,
   # FIXME(Qyriad): is this right?
@@ -78,7 +79,7 @@ configure_file(
 )
 
 liblixfetchers = declare_dependency(
-  include_directories : include_directories('.'),
+  include_directories : include_directories('.', '../include'),
   sources : libfetchers_settings_header,
   link_with : libfetchers,
 )
@@ -86,7 +87,7 @@ liblixfetchers = declare_dependency(
 # FIXME: remove when https://git.lix.systems/lix-project/lix/issues/359 is fixed.
 if is_static
   liblixfetchers_mstatic = declare_dependency(
-    include_directories : include_directories('.'),
+    include_directories : include_directories('.', '../include'),
     sources : libfetchers_settings_header,
     link_whole : libfetchers,
   )
diff --git a/src/libmain/meson.build b/src/libmain/meson.build
index a1a888c16..35633b611 100644
--- a/src/libmain/meson.build
+++ b/src/libmain/meson.build
@@ -22,6 +22,7 @@ libmain = library(
     liblixutil,
     liblixstore,
   ],
+  include_directories : [ '../include' ],
   cpp_pch : cpp_pch,
   install : true,
   # FIXME(Qyriad): is this right?
@@ -31,7 +32,7 @@ libmain = library(
 install_headers(libmain_headers, subdir : 'lix/libmain', preserve_path : true)
 
 liblixmain = declare_dependency(
-  include_directories : include_directories('.'),
+  include_directories : include_directories('.', '../include'),
   link_with : libmain,
 )
 
diff --git a/src/libstore/meson.build b/src/libstore/meson.build
index 04bdf70dd..4c9ce5c63 100644
--- a/src/libstore/meson.build
+++ b/src/libstore/meson.build
@@ -349,6 +349,7 @@ libstore = library(
   libstore_sources,
   libstore_settings_headers,
   libstore_generated_headers,
+  include_directories : [ '../include' ],
   dependencies : dependencies,
   cpp_args : cpp_args,
   cpp_pch : cpp_pch,
@@ -361,7 +362,8 @@ install_headers(libstore_headers, subdir : 'lix/libstore', preserve_path : true)
 
 # Used by libfetchers.
 liblixstore = declare_dependency(
-  include_directories : include_directories('.'),
+  # FIXME(jade): remove old '.' include directory
+  include_directories : include_directories('.', '../include'),
   sources : libstore_settings_headers,
   link_with : libstore,
 )
@@ -369,7 +371,7 @@ liblixstore = declare_dependency(
 # FIXME: remove when https://git.lix.systems/lix-project/lix/issues/359 is fixed.
 if is_static
   liblixstore_mstatic = declare_dependency(
-    include_directories : include_directories('.'),
+    include_directories : include_directories('.', '../include'),
     sources : libstore_settings_headers,
     link_whole : libstore,
   )
diff --git a/src/libutil/meson.build b/src/libutil/meson.build
index 5aec64416..cd46f512a 100644
--- a/src/libutil/meson.build
+++ b/src/libutil/meson.build
@@ -292,6 +292,7 @@ libutil = library(
     openssl,
     nlohmann_json,
   ],
+  include_directories : [ '../include' ],
   cpp_pch : cpp_pch,
   implicit_include_directories : true,
   install : true,
@@ -315,7 +316,8 @@ configure_file(
 
 # Used by libstore and libfetchers.
 liblixutil = declare_dependency(
-  include_directories : include_directories('.'),
+  # FIXME(jade): remove old "." include-dir
+  include_directories : include_directories('.', '../include'),
   sources : [
     experimental_features_header,
     deprecated_features_header,
@@ -327,7 +329,7 @@ liblixutil = declare_dependency(
 # FIXME: remove when https://git.lix.systems/lix-project/lix/issues/359 is fixed.
 if is_static
   liblixutil_mstatic = declare_dependency(
-    include_directories : include_directories('.'),
+    include_directories : include_directories('.', '../include'),
     sources : [
       experimental_features_header,
       deprecated_features_header,
diff --git a/subprojects/lix-clang-tidy/FixIncludes.cc b/subprojects/lix-clang-tidy/FixIncludes.cc
index 602d3d355..2ebeaacdf 100644
--- a/subprojects/lix-clang-tidy/FixIncludes.cc
+++ b/subprojects/lix-clang-tidy/FixIncludes.cc
@@ -58,7 +58,9 @@ void FixIncludesCallbacks::InclusionDirective(
   };
 
   for (const auto &SourceDir : SourceDirs) {
-    const bool IsAlreadyFixed = FileName.starts_with("lix/lib");
+    // Ignore generated files, since they are often only used internally within
+    // a library anyhow and they are not in the normal source dir.
+    const bool IsAlreadyFixed = FileName.starts_with("lix/lib") || FileName.contains(".gen.") || FileName.ends_with(".md");
     if (File && File->getNameAsRequested().contains(SourceDir) &&
         !IsAlreadyFixed) {
       StringRef Name = File->getNameAsRequested();