fix: key the host PCM cache on source content, add clean, hash project args

Three follow-ons to the stale-build report, all cases of an identity not
capturing something that changes the output.

The host PCM cache under <cache>/crafter.build/<target>-<march>/ is shared by
every crafter-build on the machine, and freshness was a per-file mtime
comparison. That cannot tell "this PCM is newer than my source" from "this PCM
was built from different sources that happen to be newer", so a package install
and a working checkout — or two checkouts of different versions — silently
compiled their project.cpp against each other's declarations. Invalidation now
keys on a stamp over the bytes of every module source, which also covers the
case one file's mtime never could: the cached PCMs import each other, so a
change to :Interface invalidates :Clang's PCM with Crafter.Build-Clang.cppm
untouched.

Project args ApplyStandardArgs does not itself interpret are now folded into
VariantId. Such a flag typically decides what gets compiled or bundled — the
report's example is --no-webgpu dropping entries from cfg.files — and without it
both settings shared one bin dir and interleaved their outputs there, leaving a
bundle matching neither. Sorted and deduplicated so flag order doesn't split the
cache, and inherited by test Configurations.

`crafter-build clean` removes the project's bin/ and build/ trees. It
deliberately does not load project.cpp: cleaning is most often reached when
something is already wrong, and a clean that first needs the project to compile
is useless exactly then.

implementations/Crafter.Build-Clang.cpp

@@ -63,22 +63,22 @@ namespace {
 }
 
 void Configuration::ResolvePendingImports() {
-    // Discard the local-module hits: a name recorded as pending already failed
+    // Same resolution the scan used, and against both dependency kinds — a
-    // to match this Configuration's own interfaces, and nothing adds interfaces
+    // second GetInterfacesAndImplementations call can add interfaces that an
-    // between the scan and here. Only the external edge can newly appear.
+    // earlier batch's import was looking for, so a pending name may land on a
-    std::vector<Module*> ignored;
+    // local module and not just an external one.
-    auto sweep = [this, &ignored](std::vector<std::string>& pending, std::vector<std::pair<Module*, fs::path>>& externalDeps) {
+    auto sweep = [this](std::vector<std::string>& pending, std::vector<Module*>& localDeps, std::vector<std::pair<Module*, fs::path>>& externalDeps) {
         std::erase_if(pending, [&](const std::string& name) {
-            return ResolveImportName(*this, name, ignored, externalDeps);
+            return ResolveImportName(*this, name, localDeps, externalDeps);
         });
     };
     for(const std::unique_ptr<Module>& interface : interfaces) {
         for(const std::unique_ptr<ModulePartition>& partition : interface->partitions) {
-            sweep(partition->pendingImports, partition->externalModuleDependencies);
+            sweep(partition->pendingImports, partition->moduleDependencies, partition->externalModuleDependencies);
         }
     }
     for(Implementation& implementation : implementations) {
-        sweep(implementation.pendingImports, implementation.externalModuleDependencies);
+        sweep(implementation.pendingImports, implementation.moduleDependencies, implementation.externalModuleDependencies);
     }
 }
 
@@ -1446,7 +1446,15 @@ ArgQuery Crafter::ApplyStandardArgs(Configuration& cfg, std::span<const std::str
         else if (a.starts_with("--march=")) cfg.march = std::string(a.substr(std::string_view("--march=").size()));
         else if (a.starts_with("--mtune=")) cfg.mtune = std::string(a.substr(std::string_view("--mtune=").size()));
         else if (a.starts_with("--sysroot=")) cfg.sysroot = std::string(a.substr(std::string_view("--sysroot=").size()));
+        // Anything else is the project's own flag. Its effect on the output is
+        // opaque to the framework, so it has to key into VariantId or two flag
+        // settings share a bin dir and leave a bundle matching neither.
+        else cfg.projectArgs.emplace_back(a);
     }
+    // Sorted and deduplicated so the identity depends on the set of flags, not
+    // on how they were ordered or repeated.
+    std::ranges::sort(cfg.projectArgs);
+    cfg.projectArgs.erase(std::ranges::unique(cfg.projectArgs).begin(), cfg.projectArgs.end());
     if (sawLib && cfg.type == ConfigurationType::Executable) cfg.type = ConfigurationType::LibraryStatic;
     if (sawShared && cfg.type == ConfigurationType::LibraryStatic) cfg.type = ConfigurationType::LibraryDynamic;
     // WASI sysroot autodetect, applied at config-load time so the VariantId
@@ -1461,6 +1469,21 @@ ArgQuery Crafter::ApplyStandardArgs(Configuration& cfg, std::span<const std::str
     return ArgQuery{args};
 }
 
+std::vector<fs::path> Crafter::CleanProject(const fs::path& projectFile) {
+    fs::path projectDir = fs::absolute(projectFile).lexically_normal().parent_path();
+    std::vector<fs::path> removed;
+    for (std::string_view name : { "bin", "build" }) {
+        fs::path dir = projectDir / name;
+        std::error_code ec;
+        if (!fs::is_directory(dir, ec)) continue;
+        if (fs::remove_all(dir, ec) == static_cast<std::uintmax_t>(-1) || ec) {
+            throw std::runtime_error(std::format("could not remove {}: {}", dir.string(), ec.message()));
+        }
+        removed.push_back(std::move(dir));
+    }
+    return removed;
+}
+
 static void PrintHelp(std::string_view argv0) {
     std::println(
 R"(Usage:
@@ -1468,6 +1491,7 @@ R"(Usage:
   {0} test [test-options] [globs...]    Build and run the project's tests
   {0} lint [lint-options] [globs...]    Run the project's lint rules over its sources
   {0} format [format-options] [globs...]  Apply the project's transform rules (rewrites files)
+  {0} clean                             Delete the project's bin/ and build/ trees
   {0} help | -h | --help                Show this help
 
 Loads ./project.cpp (override with --project=<path>), compiles it to a shared
@@ -1510,10 +1534,17 @@ Format options (after the `format` subcommand):
   transform. `format` rewrites changed files in place; `lint` reports the
   same transforms as would-reformat findings without writing.
 
+Clean (after the `clean` subcommand):
+  Removes bin/ and build/ next to the project file. Does not load project.cpp,
+  so it works when the project itself no longer compiles. Every target, variant
+  and dependency artifact under those trees goes with it.
+
 Project args:
   Any flag not consumed above is forwarded verbatim to CrafterBuildProject as
   part of its `args` span. Project-specific flags (e.g. --target=, custom
-  feature toggles) live there.
+  feature toggles) live there. Flags ApplyStandardArgs does not itself
+  interpret are folded into the variant hash, so switching one lands in its own
+  bin/ and build/ directory instead of overwriting the other setting's.
 
 Environment:
   CRAFTER_BUILD_MARCH                  Override -march (default: native).
@@ -1541,6 +1572,7 @@ int Crafter::Run(int argc, char** argv) {
         bool runTests = false;
         bool runLint = false;
         bool runFormat = false;
+        bool runClean = false;
         bool runAfterBuild = false;
         RunTestsOptions testOpts;
         RunLintOptions lintOpts;
@@ -1551,11 +1583,13 @@ int Crafter::Run(int argc, char** argv) {
             if (arg == "-h" || arg == "--help" || (!runTests && !runLint && !runFormat && arg == "help")) {
                 PrintHelp(argv0);
                 return 0;
-            } else if (!runLint && !runFormat && arg == "test") {
+            } else if (!runLint && !runFormat && !runClean && arg == "test") {
                 runTests = true;
-            } else if (!runTests && !runFormat && arg == "lint") {
+            } else if (!runTests && !runFormat && !runClean && arg == "lint") {
                 runLint = true;
-            } else if (!runTests && !runLint && arg == "format") {
+            } else if (!runTests && !runLint && !runClean && arg == "clean") {
+                runClean = true;
+            } else if (!runTests && !runLint && !runClean && arg == "format") {
                 runFormat = true;
                 lintOpts.mode = LintMode::Apply;
             } else if (runFormat && arg == "--check") {
@@ -1603,6 +1637,17 @@ int Crafter::Run(int argc, char** argv) {
             return 1;
         }
 
+        // Ahead of LoadProject on purpose — see CleanProject.
+        if (runClean) {
+            std::vector<fs::path> removed = CleanProject(projectFile);
+            if (removed.empty()) {
+                std::println("Nothing to clean");
+            } else {
+                for (const fs::path& dir : removed) std::println("Removed {}", dir.string());
+            }
+            return 0;
+        }
+
         Configuration config = LoadProject(projectFile, projectArgs);
         SetParentProject(&config);
 

implementations/Crafter.Build-Platform.cpp

@@ -74,6 +74,54 @@ namespace {
         CacheLock(const CacheLock&) = delete;
         CacheLock& operator=(const CacheLock&) = delete;
     };
+
+    // The cached Crafter.Build PCMs are keyed by `<target>-<march>` alone, so
+    // every crafter-build on the machine writes to the same files regardless of
+    // which share/crafter-build its module sources came from. Freshness used to
+    // be a per-file mtime comparison, which cannot distinguish "this PCM is
+    // newer than my source" from "this PCM was built from *different* sources
+    // that happen to be newer" — so a second install or checkout silently
+    // compiled its project against the other's declarations. Same failure shape
+    // as issue #27: no error, a binary built against a layout nobody linked.
+    //
+    // A stamp over the bytes of every module source answers what the mtime
+    // can't. It covers the whole set rather than one file at a time because the
+    // PCMs import each other: a change to :Interface invalidates :Clang's PCM
+    // even though Crafter.Build-Clang.cppm is untouched.
+    std::string CrafterBuildSourceStamp(const fs::path& sourceDir, std::span<const std::string_view> moduleNames) {
+        std::string all;
+        auto append = [&all, &sourceDir](const fs::path& relative) {
+            std::ifstream in(sourceDir / relative, std::ios::binary);
+            std::ostringstream buffer;
+            buffer << in.rdbuf();
+            all += relative.string();
+            all += '\0';
+            all += buffer.str();
+            all += '\0';
+        };
+        for (std::string_view name : moduleNames) {
+            append(fs::path(std::format("{}.cppm", name)));
+        }
+        // Exported through `module;` preambles, so its contents land in the PCMs
+        // too.
+        append("Crafter.Build-Api.h");
+        return std::format("{:016x}", std::hash<std::string>{}(all));
+    }
+
+    fs::path CacheStampPath(const fs::path& cacheDir) {
+        return cacheDir / "crafter-build-sources.stamp";
+    }
+
+    std::string ReadCacheStamp(const fs::path& cacheDir) {
+        std::ifstream in(CacheStampPath(cacheDir), std::ios::binary);
+        std::string stamp;
+        std::getline(in, stamp);
+        return stamp;
+    }
+
+    void WriteCacheStamp(const fs::path& cacheDir, const std::string& stamp) {
+        std::ofstream(CacheStampPath(cacheDir), std::ios::binary | std::ios::trunc) << stamp << '\n';
+    }
 }
 
 fs::path Crafter::GetCrafterBuildHome() {
@@ -328,13 +376,17 @@ std::string Crafter::GetBaseCommand(const Configuration& config) {
 namespace {
     void EnsureCrafterBuildPcms(const fs::path& sourceDir, const fs::path& cacheDir) {
         CacheLock lock(cacheDir);
+        // Re-derived under the lock: another builder may have refreshed the
+        // cache from its own sources while we waited.
+        std::string stamp = CrafterBuildSourceStamp(sourceDir, CrafterBuildModules);
+        bool upToDate = ReadCacheStamp(cacheDir) == stamp;
         for (std::string_view name : CrafterBuildModules) {
             fs::path cppmPath = sourceDir / std::format("{}.cppm", name);
             fs::path pcmPath = cacheDir / std::format("{}.pcm", name);
             if (!fs::exists(cppmPath)) {
                 throw std::runtime_error(std::format("module source {} not found in {} (set CRAFTER_BUILD_HOME)", name, sourceDir.string()));
             }
-            if (fs::exists(pcmPath) && fs::last_write_time(cppmPath) < fs::last_write_time(pcmPath)) {
+            if (upToDate && fs::exists(pcmPath)) {
                 continue;
             }
             std::string cmd = std::format(
@@ -350,6 +402,10 @@ namespace {
                 throw std::runtime_error(std::format("Failed to precompile {} (exit {}): {}", name, r.exitCode, r.output));
             }
         }
+        // Last, so an interrupted rebuild leaves the stamp disagreeing with the
+        // sources and the next run starts over rather than trusting a half-built
+        // set of PCMs.
+        if (!upToDate) WriteCacheStamp(cacheDir, stamp);
     }
 }
 
@@ -523,6 +579,10 @@ std::string Crafter::GetBaseCommand(const Configuration& config) {
 namespace {
     void EnsureCrafterBuildPcms(const fs::path& sourceDir, const fs::path& cacheDir) {
         CacheLock lock(cacheDir);
+        // Re-derived under the lock: another builder may have refreshed the
+        // cache from its own sources while we waited.
+        std::string stamp = CrafterBuildSourceStamp(sourceDir, CrafterBuildModules);
+        bool upToDate = ReadCacheStamp(cacheDir) == stamp;
         fs::path prefix = MingwPrefix();
         for (std::string_view name : CrafterBuildModules) {
             fs::path cppmPath = sourceDir / std::format("{}.cppm", name);
@@ -530,7 +590,7 @@ namespace {
             if (!fs::exists(cppmPath)) {
                 throw std::runtime_error(std::format("module source {} not found in {} (set CRAFTER_BUILD_HOME)", name, sourceDir.string()));
             }
-            if (fs::exists(pcmPath) && fs::last_write_time(cppmPath) < fs::last_write_time(pcmPath)) {
+            if (upToDate && fs::exists(pcmPath)) {
                 continue;
             }
             std::string cmd = std::format(
@@ -546,6 +606,10 @@ namespace {
                 throw std::runtime_error(std::format("Failed to precompile {} (exit {}): {}", name, r.exitCode, r.output));
             }
         }
+        // Last, so an interrupted rebuild leaves the stamp disagreeing with the
+        // sources and the next run starts over rather than trusting a half-built
+        // set of PCMs.
+        if (!upToDate) WriteCacheStamp(cacheDir, stamp);
     }
 }
 
@@ -839,13 +903,17 @@ namespace {
 
     void EnsureCrafterBuildPcms(const fs::path& sourceDir, const fs::path& cacheDir) {
         CacheLock lock(cacheDir);
+        // Re-derived under the lock: another builder may have refreshed the
+        // cache from its own sources while we waited.
+        std::string stamp = CrafterBuildSourceStamp(sourceDir, CrafterBuildModules);
+        bool upToDate = ReadCacheStamp(cacheDir) == stamp;
         for (std::string_view name : CrafterBuildModules) {
             fs::path cppmPath = sourceDir / std::format("{}.cppm", name);
             fs::path pcmPath = cacheDir / std::format("{}.pcm", name);
             if (!fs::exists(cppmPath)) {
                 throw std::runtime_error(std::format("module source {} not found in {} (set CRAFTER_BUILD_HOME)", name, sourceDir.string()));
             }
-            if (fs::exists(pcmPath) && fs::last_write_time(cppmPath) < fs::last_write_time(pcmPath)) {
+            if (upToDate && fs::exists(pcmPath)) {
                 continue;
             }
             std::string cmd = std::format(
@@ -860,6 +928,10 @@ namespace {
                 throw std::runtime_error(std::format("Failed to precompile {} (exit {}): {}", name, r.exitCode, r.output));
             }
         }
+        // Last, so an interrupted rebuild leaves the stamp disagreeing with the
+        // sources and the next run starts over rather than trusting a half-built
+        // set of PCMs.
+        if (!upToDate) WriteCacheStamp(cacheDir, stamp);
     }
 }
 

implementations/Crafter.Build-Test.cpp

@@ -429,6 +429,10 @@ TestBuilder Configuration::AddTest(std::string_view name, std::span<fs::path> in
     t.config.mtune = this->mtune;
     t.config.sysroot = this->sysroot;
     t.config.debug = this->debug;
+    // Inherited so a project flag that changes what the library contains also
+    // moves the test's own outputs, rather than letting two flag settings share
+    // one test bin dir.
+    t.config.projectArgs = this->projectArgs;
     t.config.type = ConfigurationType::Executable;
 
     // Default source layout: tests/<name>/main.cpp resolved against the
@@ -453,6 +457,7 @@ void Configuration::AddMarchVariants(std::string_view name, std::span<fs::path>
         t.config.mtune = tier.mtune;
         t.config.sysroot = this->sysroot;
         t.config.debug = this->debug;
+        t.config.projectArgs = this->projectArgs;
         t.config.type = ConfigurationType::Executable;
 
         fs::path mainSource = fs::path("tests") / std::string(name) / "main";

interfaces/Crafter.Build-Clang.cppm

@@ -250,6 +250,15 @@ export namespace Crafter {
         // clobber the baseline's. Not for direct project use — declare
         // wasmVariants instead.
         std::vector<std::string> wasmVariantFlags;
+        // The project args ApplyStandardArgs did not interpret — i.e. the
+        // project's own flags, whose effect on the build the framework cannot
+        // see. Hashed into VariantId because such a flag typically decides what
+        // gets compiled or bundled (`--no-webgpu` dropping entries from
+        // cfg.files, say), and without it both flag settings share one bin dir
+        // and interleave their outputs there. Populated by ApplyStandardArgs;
+        // the args it does recognise are excluded, since their effect already
+        // shows up in target/march/mtune/debug/sysroot/type.
+        std::vector<std::string> projectArgs;
         std::vector<Test> tests;
         // Lint rules for `crafter-build lint`. Populate via AddLintRule.
         std::vector<LintRule> lintRules;
@@ -315,6 +324,12 @@ export namespace Crafter {
                 compileKey += "|W:";
                 compileKey += f;
             }
+            // Sorted by ApplyStandardArgs, so flag order on the command line
+            // doesn't split the cache.
+            for (const std::string& a : projectArgs) {
+                compileKey += "|A:";
+                compileKey += a;
+            }
             std::size_t configHash = std::hash<std::string>{}(compileKey);
             return std::format("{}-{}-{}-{}-{:08x}", name, target, march, mtune, configHash);
         }
@@ -345,6 +360,16 @@ export namespace Crafter {
 
     CRAFTER_API int Run(int argc, char** argv);
 
+    // Delete the bin/ and build/ trees beside `projectFile`, returning the paths
+    // that existed and were removed. Backs `crafter-build clean`.
+    //
+    // Deliberately does not load the project: cleaning is most often reached
+    // when something is already wrong, and a clean that first needs project.cpp
+    // to compile (and its git dependencies to be present) is useless exactly
+    // then. That means variant directories are not enumerated — the whole tree
+    // goes, which is what the by-hand `rm -rf bin build` did anyway.
+    CRAFTER_API std::vector<fs::path> CleanProject(const fs::path& projectFile);
+
     // Add a small index.html + runtime.js pair next to the .wasm output so the
     // build can be loaded directly in a browser (just `serve` the bin dir and
     // open it). Opt-in: WASI builds destined for wasmtime/wasmer don't need

project.cpp

@@ -108,6 +108,7 @@ extern "C" Configuration CrafterBuildProject(std::span<const std::string_view> a
         cfg.AddTest("ModuleInterface").Dependencies({ CrafterBuildLib.get() });
         cfg.AddTest("DependencyLink").Dependencies({ CrafterBuildLib.get() });
         cfg.AddTest("IncrementalInterfaceChange").Dependencies({ CrafterBuildLib.get() });
+        cfg.AddTest("CleanProject").Dependencies({ CrafterBuildLib.get() });
         cfg.AddTest("ShaderCompile").Dependencies({ CrafterBuildLib.get() });
         cfg.AddTest("StandardArgs").Dependencies({ CrafterBuildLib.get() });
         cfg.AddTest("TestRunnerSpec").Dependencies({ CrafterBuildLib.get() });
@@ -121,6 +122,9 @@ extern "C" Configuration CrafterBuildProject(std::span<const std::string_view> a
         // for project.so.
         cfg.AddTest("ConcurrentCacheRace").Dependencies({ CrafterBuildLib.get() })
             .LinkFlag("-Wl,--export-dynamic").LinkFlag("-ldl");
+        // Same LoadProject wiring as ConcurrentCacheRace above.
+        cfg.AddTest("HostCacheSourceStamp").Dependencies({ CrafterBuildLib.get() })
+            .LinkFlag("-Wl,--export-dynamic").LinkFlag("-ldl");
         cfg.AddTest("ConcurrentDependencyReset").Dependencies({ CrafterBuildLib.get() });
         cfg.AddTest("Lint").Dependencies({ CrafterBuildLib.get() });
         cfg.AddTest("HouseRules").Dependencies({ CrafterBuildLib.get() });

tests/CleanProject/main.cpp

@@ -0,0 +1,79 @@
+// SPDX-License-Identifier: LGPL-3.0-only
+// SPDX-FileCopyrightText: Copyright (C) 2026 Catcrafts®
+
+import std;
+import Crafter.Build;
+namespace fs = std::filesystem;
+using namespace Crafter;
+
+// `crafter-build clean` exists so the fix for a stale build is discoverable
+// rather than folklore. It must not need the project to load: the state you most
+// want to clear is one where the build is already broken.
+namespace {
+    std::int32_t Failures = 0;
+
+    void Check(bool cond, std::string_view msg) {
+        if (!cond) {
+            std::println(std::cerr, "FAIL: {}", msg);
+            ++Failures;
+        }
+    }
+
+    fs::path StageProject(std::string_view leaf) {
+        fs::path root = fs::temp_directory_path() / std::format("crafter-build-clean-{}", leaf);
+        fs::remove_all(root);
+        fs::create_directories(root / "bin" / "app-x86_64-pc-linux-gnu-native-native-0badf00d");
+        fs::create_directories(root / "build" / "app-x86_64-pc-linux-gnu-native-native-0badf00d");
+        std::ofstream(root / "bin" / "app-x86_64-pc-linux-gnu-native-native-0badf00d" / "app") << "binary";
+        std::ofstream(root / "build" / "app-x86_64-pc-linux-gnu-native-native-0badf00d" / "main_impl.o") << "object";
+        std::ofstream(root / "keep-me.txt") << "untouched";
+        return root;
+    }
+}
+
+int main() {
+    {
+        // A project file that could never compile: clean has to work anyway.
+        fs::path root = StageProject("broken");
+        fs::path projectFile = root / "project.cpp";
+        std::ofstream(projectFile) << "this is not valid C++ at all\n";
+
+        std::vector<fs::path> removed = CleanProject(projectFile);
+        Check(removed.size() == 2, std::format("both trees reported removed, got {}", removed.size()));
+        Check(!fs::exists(root / "bin"), "bin/ is gone");
+        Check(!fs::exists(root / "build"), "build/ is gone");
+        Check(fs::exists(root / "keep-me.txt"), "unrelated files in the project root are left alone");
+        Check(fs::exists(projectFile), "the project file itself is left alone");
+    }
+
+    {
+        // Idempotent, and quiet about it — nothing to remove is not an error.
+        fs::path root = StageProject("twice");
+        fs::path projectFile = root / "project.cpp";
+        std::ofstream(projectFile) << "\n";
+
+        CleanProject(projectFile);
+        std::vector<fs::path> second = CleanProject(projectFile);
+        Check(second.empty(), "a second clean reports nothing removed");
+    }
+
+    {
+        // Resolved relative to the project file, not the cwd, so --project=
+        // cleans the project it names.
+        fs::path root = StageProject("elsewhere");
+        fs::path projectFile = root / "project.cpp";
+        std::ofstream(projectFile) << "\n";
+        fs::path cwdBin = fs::current_path() / "bin";
+        bool cwdBinExisted = fs::exists(cwdBin);
+
+        CleanProject(projectFile);
+        Check(!fs::exists(root / "bin"), "the named project's bin/ is gone");
+        Check(fs::exists(cwdBin) == cwdBinExisted, "the cwd's bin/ is untouched");
+    }
+
+    if (Failures > 0) {
+        std::println(std::cerr, "{} assertions failed", Failures);
+        return 1;
+    }
+    return 0;
+}

tests/HostCacheSourceStamp/main.cpp

@@ -0,0 +1,150 @@
+// SPDX-License-Identifier: LGPL-3.0-only
+// SPDX-FileCopyrightText: Copyright (C) 2026 Catcrafts®
+
+#include <stdlib.h>
+import std;
+import Crafter.Build;
+namespace fs = std::filesystem;
+using namespace Crafter;
+
+// The host PCM cache is keyed by `<target>-<march>` alone, so every
+// crafter-build on a machine — a package install and a working checkout, two
+// checkouts of different versions — writes the same `Crafter.Build-*.pcm`
+// files. Freshness was a per-file mtime comparison, which says "the PCM is
+// newer than my source, reuse it" whether or not it was built from *my*
+// source. The loser then compiled its project.cpp against the other install's
+// declarations: no error, and a project.so built against a layout that doesn't
+// match the library it's loaded into — the same silent shape as issue #27.
+//
+// So the invalidation has to key on the source bytes, and this test asserts it
+// notices a change the mtime rule provably cannot see: different content with a
+// deliberately *older* timestamp.
+namespace {
+    std::int32_t Failures = 0;
+
+    void Check(bool cond, std::string_view msg) {
+        if (!cond) {
+            std::println(std::cerr, "FAIL: {}", msg);
+            ++Failures;
+        }
+    }
+
+    // The cache subdirectory is named for the host target and march; glob for
+    // it rather than reconstructing the naming rule here.
+    fs::path FindModuleCacheDir(const fs::path& cacheRoot) {
+        for (const fs::directory_entry& entry : fs::directory_iterator(cacheRoot / "crafter.build")) {
+            if (entry.is_directory()) return entry.path();
+        }
+        return {};
+    }
+
+    std::string ReadStamp(const fs::path& moduleCacheDir) {
+        std::ifstream in(moduleCacheDir / "crafter-build-sources.stamp");
+        std::string stamp;
+        std::getline(in, stamp);
+        return stamp;
+    }
+}
+
+int main() {
+    fs::path installedHome = GetCrafterBuildHome();
+    if (!fs::exists(installedHome / "Crafter.Build.cppm")) {
+        std::println(std::cerr, "SKIP: no module sources at {}", installedHome.string());
+        return 77;
+    }
+
+    fs::path scratch = fs::temp_directory_path() / "crafter-build-host-cache-source-stamp";
+    std::error_code ec;
+    fs::remove_all(scratch, ec);
+    fs::create_directories(scratch);
+
+    // A private copy of the module sources, so the mutation below can't touch
+    // the real install, and a cold private cache so the first LoadProject has
+    // to populate it.
+    fs::path home = scratch / "share" / "crafter-build";
+    fs::create_directories(home.parent_path());
+    fs::copy(installedHome, home, fs::copy_options::recursive);
+    setenv("CRAFTER_BUILD_HOME", home.string().c_str(), 1);
+
+    fs::path cacheRoot = scratch / "cache";
+    fs::create_directories(cacheRoot);
+    setenv("XDG_CACHE_HOME", cacheRoot.string().c_str(), 1);
+
+    fs::path projectDir = scratch / "project";
+    fs::create_directories(projectDir);
+    fs::path projectFile = projectDir / "project.cpp";
+    std::ofstream(projectFile) <<
+        "import std;\n"
+        "import Crafter.Build;\n"
+        "using namespace Crafter;\n"
+        "extern \"C\" Configuration CrafterBuildProject(std::span<const std::string_view>) {\n"
+        "    Configuration cfg;\n"
+        "    cfg.path = \"./\";\n"
+        "    cfg.name = \"stamped\";\n"
+        "    cfg.outputName = \"stamped\";\n"
+        "    cfg.target = HostTarget();\n"
+        "    cfg.type = ConfigurationType::Executable;\n"
+        "    return cfg;\n"
+        "}\n";
+
+    std::array<std::string_view, 0> noArgs = {};
+
+    try {
+        (void)LoadProject(projectFile, noArgs);
+    } catch (const std::exception& e) {
+        std::println(std::cerr, "FAIL: first LoadProject threw: {}", e.what());
+        return 1;
+    }
+
+    fs::path moduleCacheDir = FindModuleCacheDir(cacheRoot);
+    Check(!moduleCacheDir.empty(), "a module cache directory was created");
+    if (moduleCacheDir.empty()) return 1;
+
+    fs::path probePcm = moduleCacheDir / "Crafter.Build-Clang.pcm";
+    Check(fs::exists(probePcm), "the cold run populated the cache");
+    if (!fs::exists(probePcm)) return 1;
+
+    std::string firstStamp = ReadStamp(moduleCacheDir);
+    Check(!firstStamp.empty(), "the cold run recorded a source stamp");
+    fs::file_time_type afterCold = fs::last_write_time(probePcm);
+
+    // Unchanged sources must be a no-op — the stamp is an invalidation key, not
+    // an excuse to precompile eleven modules on every invocation.
+    try {
+        (void)LoadProject(projectFile, noArgs);
+    } catch (const std::exception& e) {
+        std::println(std::cerr, "FAIL: warm LoadProject threw: {}", e.what());
+        return 1;
+    }
+    Check(fs::last_write_time(probePcm) == afterCold, "unchanged sources do not rebuild the cache");
+    Check(ReadStamp(moduleCacheDir) == firstStamp, "unchanged sources keep the same stamp");
+
+    // Now the case the mtime rule cannot see. The edit lands in a module the
+    // probe does not name, because the cached PCMs import each other: a change
+    // anywhere in the set invalidates all of them.
+    fs::path edited = home / "Crafter.Build-Progress.cppm";
+    {
+        std::ofstream append(edited, std::ios::app);
+        append << "\n// Content change with a backdated timestamp.\n";
+    }
+    fs::last_write_time(edited, afterCold - std::chrono::hours(24));
+    Check(fs::last_write_time(edited) < fs::last_write_time(probePcm), "the edited source really is older than the cached PCM");
+
+    try {
+        (void)LoadProject(projectFile, noArgs);
+    } catch (const std::exception& e) {
+        std::println(std::cerr, "FAIL: LoadProject after the edit threw: {}", e.what());
+        return 1;
+    }
+
+    Check(fs::last_write_time(probePcm) > afterCold, "a content change rebuilds the cache even when the source's mtime is older");
+    Check(ReadStamp(moduleCacheDir) != firstStamp, "the recorded stamp follows the sources");
+
+    fs::remove_all(scratch, ec);
+
+    if (Failures > 0) {
+        std::println(std::cerr, "{} assertions failed", Failures);
+        return 1;
+    }
+    return 0;
+}

tests/StandardArgs/main.cpp

@@ -83,6 +83,31 @@ int main() {
         Check(!q.Get("--other=").has_value(), "ArgQuery::Get returns nullopt for absent prefix");
     }
 
+    // Flags ApplyStandardArgs doesn't itself interpret are collected into
+    // cfg.projectArgs, which feeds VariantId — a project flag that changes what
+    // gets compiled has to move the output directory with it.
+    {
+        Configuration cfg;
+        std::array<std::string_view, 5> raw = {
+            "--debug", "--no-webgpu", "--target=aarch64-linux-gnu", "--feature=fancy", "bare",
+        };
+        ApplyStandardArgs(cfg, raw);
+        std::vector<std::string> expected = { "--feature=fancy", "--no-webgpu", "bare" };
+        Check(cfg.projectArgs == expected, std::format("only unrecognised args are collected, sorted; got [{}]", std::format("{}", std::views::join_with(cfg.projectArgs, std::string(", ")) | std::ranges::to<std::string>())));
+    }
+
+    // Order and repetition must not perturb the set — otherwise the same build
+    // spelled two ways would land in two directories.
+    {
+        Configuration a;
+        Configuration b;
+        std::array<std::string_view, 2> forward = { "--alpha", "--beta" };
+        std::array<std::string_view, 3> reversed = { "--beta", "--alpha", "--beta" };
+        ApplyStandardArgs(a, forward);
+        ApplyStandardArgs(b, reversed);
+        Check(a.projectArgs == b.projectArgs, "projectArgs is order- and duplicate-insensitive");
+    }
+
     if (Failures > 0) {
         std::println(std::cerr, "{} assertions failed", Failures);
         return 1;

tests/VariantId/main.cpp

@@ -96,6 +96,25 @@ int main() {
         b.march = "x86-64-v3";
         Check(a.VariantId() != b.VariantId(), "march change perturbs VariantId");
     }
+    {
+        // A project flag the framework can't interpret still decides what gets
+        // compiled and bundled, so it has to key into VariantId. Otherwise both
+        // settings share one bin dir and interleave their outputs there — an
+        // index.html from one alongside a script from the other.
+        Configuration a = MakeBase();
+        Configuration b = MakeBase();
+        b.projectArgs.push_back("--no-webgpu");
+        Check(a.VariantId() != b.VariantId(), "project arg perturbs VariantId");
+        Check(a.BinDir() != b.BinDir(), "project arg yields a distinct BinDir");
+    }
+    {
+        // Distinct project args must not collide with each other either.
+        Configuration a = MakeBase();
+        a.projectArgs.push_back("--no-webgpu");
+        Configuration b = MakeBase();
+        b.projectArgs.push_back("--no-audio");
+        Check(a.VariantId() != b.VariantId(), "different project args yield different VariantId");
+    }
     {
         // PcmDir() differs between Executable (in BuildDir) and Library
         // (in BinDir) — Library PCMs land in the installable bin dir so