fix: resolve multiple CI failures

.github/workflows/ci.yml

@@ -95,9 +95,20 @@ jobs:
       - name: Run tests (nextest)
         # thread-language's napi-* features conflict with tree-sitter-parsing at runtime;
         # run it separately with only the compatible feature set.
+        # On Linux and Windows, run all tests (Docker is available for testcontainers).
+        if: runner.os != 'macOS'
         run: |
           cargo nextest run --workspace --exclude thread-language --all-features --no-fail-fast
           cargo nextest run -p thread-language --features all-parsers,matching --no-fail-fast
+      - name: Run tests (nextest, macOS - skip Docker-dependent tests)
+        # macOS GitHub Actions runners (Apple Silicon) do not have Docker,
+        # so we exclude the incremental_postgres_tests that use testcontainers
+        # to spin up Postgres containers.
+        if: runner.os == 'macOS'
+        run: |
+          cargo nextest run --workspace --exclude thread-language --all-features --no-fail-fast \
+            -E "not (package(thread-flow) and binary(incremental_postgres_tests))"
+          cargo nextest run -p thread-language --features all-parsers,matching --no-fail-fast
       - name: Run doc tests
         run: |
           cargo test --doc --workspace --exclude thread-language --all-features
@@ -119,6 +130,133 @@ jobs:
         uses: Swatinem/rust-cache@v2
         with:
           cache-on-failure: true
+      - name: Install clang for WASM C compilation
+        run: sudo apt-get update -qq && sudo apt-get install -y clang
+      - name: Set up C header stubs for wasm32-unknown-unknown
+        # tree-sitter 0.25+ compiles C sources that #include standard C library headers
+        # (stdio.h, stdlib.h, string.h, etc.). The wasm32-unknown-unknown target has no OS
+        # and therefore no libc headers. We provide minimal stubs so the code compiles;
+        # actual implementations (malloc, memcpy, etc.) come from the wasm runtime / Rust.
+        run: |
+          CLANG_RES=$(clang --print-resource-dir)
+          STUBS=/tmp/wasm-stubs
+          mkdir -p "$STUBS"
+
+          # Use Python to write the stub files cleanly without heredoc indentation issues.
+          python3 - << 'PYEOF'
+import os
+STUBS = '/tmp/wasm-stubs'
+stubs = {}
+
+stubs['stdio.h'] = """\
+#pragma once
+#include <stddef.h>
+#include <stdarg.h>
+typedef void FILE;
+#define stderr ((FILE*)0)
+#define stdout ((FILE*)0)
+#define stdin  ((FILE*)0)
+#define EOF    (-1)
+static inline int fprintf(FILE *f, const char *fmt, ...) { (void)f; (void)fmt; return 0; }
+static inline int vfprintf(FILE *f, const char *fmt, va_list ap) { (void)f; (void)fmt; (void)ap; return 0; }
+static inline int printf(const char *fmt, ...) { (void)fmt; return 0; }
+static inline int snprintf(char *s, size_t n, const char *fmt, ...) { (void)s; (void)n; (void)fmt; return 0; }
+static inline int sprintf(char *s, const char *fmt, ...) { (void)s; (void)fmt; return 0; }
+static inline int fputc(int c, FILE *f) { (void)f; return c; }
+static inline int fputs(const char *s, FILE *f) { (void)s; (void)f; return 0; }
+static inline int fflush(FILE *f) { (void)f; return 0; }
+"""
+
+stubs['stdlib.h'] = """\
+#pragma once
+#include <stddef.h>
+#define EXIT_SUCCESS 0
+#define EXIT_FAILURE 1
+extern void *malloc(size_t size);
+extern void *calloc(size_t count, size_t size);
+extern void *realloc(void *ptr, size_t size);
+extern void  free(void *ptr);
+extern void  abort(void);
+extern void  exit(int status);
+static inline int abs(int x) { return x < 0 ? -x : x; }
+"""
+
+stubs['string.h'] = """\
+#pragma once
+#include <stddef.h>
+extern void  *memcpy(void *dest, const void *src, size_t n);
+extern void  *memmove(void *dest, const void *src, size_t n);
+extern void  *memset(void *s, int c, size_t n);
+extern int    memcmp(const void *s1, const void *s2, size_t n);
+extern void  *memchr(const void *s, int c, size_t n);
+extern size_t strlen(const char *s);
+extern int    strcmp(const char *s1, const char *s2);
+extern int    strncmp(const char *s1, const char *s2, size_t n);
+extern char  *strcpy(char *dest, const char *src);
+extern char  *strncpy(char *dest, const char *src, size_t n);
+extern char  *strcat(char *dest, const char *src);
+extern char  *strncat(char *dest, const char *src, size_t n);
+extern char  *strchr(const char *s, int c);
+extern char  *strrchr(const char *s, int c);
+extern char  *strstr(const char *haystack, const char *needle);
+"""
+
+stubs['time.h'] = """\
+#pragma once
+#include <stdint.h>
+typedef uint64_t time_t;
+typedef uint64_t clock_t;
+#define CLOCKS_PER_SEC ((clock_t)1000000)
+static inline time_t time(time_t *t) { if (t) *t = 0; return 0; }
+static inline clock_t clock(void) { return 0; }
+"""
+
+stubs['ctype.h'] = """\
+#pragma once
+static inline int isalpha(int c) { return (c>='a'&&c<='z')||(c>='A'&&c<='Z'); }
+static inline int isdigit(int c) { return c>='0'&&c<='9'; }
+static inline int isalnum(int c) { return isalpha(c)||isdigit(c); }
+static inline int isspace(int c) { return c==' '||c=='\\t'||c=='\\n'||c=='\\r'||c=='\\f'||c=='\\v'; }
+static inline int isupper(int c) { return c>='A'&&c<='Z'; }
+static inline int islower(int c) { return c>='a'&&c<='z'; }
+static inline int toupper(int c) { return islower(c)?c-('a'-'A'):c; }
+static inline int tolower(int c) { return isupper(c)?c+('a'-'A'):c; }
+static inline int isprint(int c) { return c>=' '&&c<='~'; }
+static inline int iscntrl(int c) { return c<' '||c==127; }
+static inline int isxdigit(int c) { return isdigit(c)||(c>='a'&&c<='f')||(c>='A'&&c<='F'); }
+static inline int ispunct(int c) { return isprint(c)&&!isalnum(c)&&c!=' '; }
+"""
+
+stubs['wctype.h'] = """\
+#pragma once
+#include <stdint.h>
+typedef uint32_t wint_t;
+#define WEOF ((wint_t)-1)
+static inline int     iswspace(wint_t c) { return c==' '||c=='\\t'||c=='\\n'||c=='\\r'||c=='\\f'||c=='\\v'; }
+static inline int     iswalpha(wint_t c) { return (c>='a'&&c<='z')||(c>='A'&&c<='Z'); }
+static inline int     iswdigit(wint_t c) { return c>='0'&&c<='9'; }
+static inline int     iswalnum(wint_t c) { return iswalpha(c)||iswdigit(c); }
+static inline int     iswupper(wint_t c) { return c>='A'&&c<='Z'; }
+static inline int     iswlower(wint_t c) { return c>='a'&&c<='z'; }
+static inline int     iswprint(wint_t c) { return c>=' '&&c<='~'; }
+static inline int     iswpunct(wint_t c) { return iswprint(c)&&!iswalnum(c)&&c!=' '; }
+static inline wint_t  towlower(wint_t c) { return iswupper(c)?c+('a'-'A'):c; }
+static inline wint_t  towupper(wint_t c) { return iswlower(c)?c-('a'-'A'):c; }
+"""
+
+stubs['assert.h'] = """\
+#pragma once
+#define assert(x) ((void)(x))
+"""
+
+for name, content in stubs.items():
+    path = os.path.join(STUBS, name)
+    with open(path, 'w') as f:
+        f.write(content)
+    print(f'  wrote {path}')
+PYEOF
+
+          echo "CFLAGS_wasm32_unknown_unknown=-I${STUBS} -I${CLANG_RES}/include" >> "$GITHUB_ENV"
       - name: Install wasm-pack
         uses: jetli/wasm-pack-action@v0.4.0
       - name: Build WASM (dev)
@@ -163,6 +301,9 @@ jobs:
     name: Security Audit
     needs: quick-checks
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      checks: write
     steps:
       - uses: actions/checkout@v4
         with:

REUSE.toml

@@ -8,3 +8,33 @@ path = ["claudedocs/**", "crates/**/claudedocs/**"]
 precedence = "aggregate"
 SPDX-FileCopyrightText = "2025 Knitli Inc. <knitli@knit.li>"
 SPDX-License-Identifier = "MIT OR Apache-2.0"
+
+[[annotations]]
+path = [".claude/plugins/**", "ctx-plugin/**"]
+precedence = "aggregate"
+SPDX-FileCopyrightText = "2025 Knitli Inc. <knitli@knit.li>"
+SPDX-License-Identifier = "MIT OR Apache-2.0"
+
+[[annotations]]
+path = [".vscode/**"]
+precedence = "aggregate"
+SPDX-FileCopyrightText = "2025 Knitli Inc. <knitli@knit.li>"
+SPDX-License-Identifier = "MIT OR Apache-2.0"
+
+[[annotations]]
+path = ["crates/flow/benches/bench_graph_traversal.rs"]
+precedence = "aggregate"
+SPDX-FileCopyrightText = "2025 Knitli Inc. <knitli@knit.li>"
+SPDX-License-Identifier = "AGPL-3.0-or-later"
+
+[[annotations]]
+path = ["get_comments.js"]
+precedence = "aggregate"
+SPDX-FileCopyrightText = "2025 Knitli Inc. <knitli@knit.li>"
+SPDX-License-Identifier = "MIT OR Apache-2.0"
+
+[[annotations]]
+path = ["specs/**"]
+precedence = "aggregate"
+SPDX-FileCopyrightText = "2025 Knitli Inc. <knitli@knit.li>"
+SPDX-License-Identifier = "MIT OR Apache-2.0"

crates/ast-engine/src/tree_sitter/mod.rs

@@ -145,6 +145,7 @@ fn parse_lang(
 ///
 /// ```rust,no_run
 /// # use thread_ast_engine::tree_sitter::StrDoc;
+/// # use thread_ast_engine::Doc;
 /// # #[derive(Clone, Debug)]
 /// # struct JavaScript;
 /// # impl thread_ast_engine::Language for JavaScript {

crates/flow/benches/bench_graph_traversal.rs.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: AGPL-3.0-or-later

crates/flow/src/incremental/graph.rs

@@ -260,7 +260,7 @@ impl DependencyGraph {
     /// ));
     ///
     /// // Change C -> affects B and A
-    /// let changed = RapidSet::from([PathBuf::from("C")]);
+    /// let changed: RapidSet<PathBuf> = [PathBuf::from("C")].into_iter().collect();
     /// let affected = graph.find_affected_files(&changed);
     /// assert!(affected.contains(&PathBuf::from("A")));
     /// assert!(affected.contains(&PathBuf::from("B")));
@@ -325,9 +325,9 @@ impl DependencyGraph {
     ///     PathBuf::from("B"), PathBuf::from("C"), DependencyType::Import,
     /// ));
     ///
-    /// let files = RapidSet::from([
+    /// let files: RapidSet<PathBuf> = [
     ///     PathBuf::from("A"), PathBuf::from("B"), PathBuf::from("C"),
-    /// ]);
+    /// ].into_iter().collect();
     /// let sorted = graph.topological_sort(&files).unwrap();
     /// // C should come before B, B before A
     /// let pos_a = sorted.iter().position(|p| p == &PathBuf::from("A")).unwrap();

crates/flow/src/incremental/invalidation.rs

@@ -45,7 +45,6 @@ pub enum InvalidationError {
 /// ```rust
 /// use thread_flow::incremental::invalidation::InvalidationDetector;
 /// use thread_flow::incremental::DependencyGraph;
-/// use thread_utilities::RapishSet;
 /// use std::path::PathBuf;
 ///
 /// let graph = DependencyGraph::new();

crates/flow/src/incremental/mod.rs

@@ -36,8 +36,8 @@
 //!     AnalysisDefFingerprint, DependencyEdge, DependencyType,
 //! };
 //! use thread_flow::incremental::graph::DependencyGraph;
+//! use thread_utilities::RapidSet;
 //! use std::path::PathBuf;
-//! use std::collections::HashSet;
 //!
 //! // Create a dependency graph
 //! let mut graph = DependencyGraph::new();
@@ -51,7 +51,7 @@
 //! });
 //!
 //! // Find files affected by a change to utils.rs
-//! let changed = HashSet::from([PathBuf::from("src/utils.rs")]);
+//! let changed: RapidSet<PathBuf> = [PathBuf::from("src/utils.rs")].into_iter().collect();
 //! let affected = graph.find_affected_files(&changed);
 //! assert!(affected.contains(&PathBuf::from("src/main.rs")));
 //! ```

crates/flow/src/incremental/types.rs

@@ -220,7 +220,7 @@ impl AnalysisDefFingerprint {
     /// use thread_utilities::RapidSet;
     /// use std::path::PathBuf;
     ///
-    /// let sources = RapidSet::from([PathBuf::from("dep.rs")]);
+    /// let sources: RapidSet<PathBuf> = [PathBuf::from("dep.rs")].into_iter().collect();
     /// let fp = AnalysisDefFingerprint::with_sources(b"content", sources);
     /// assert_eq!(fp.source_files.len(), 1);
     /// ```

ctx-plugin/.claude-plugin/plugin.json.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/PLAN.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/README.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/agents/claim-validator.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/agents/context-auditor.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/commands/ctx-check.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/commands/ctx-discover.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/commands/ctx-drift.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/commands/ctx-fix.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/commands/ctx.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/cross-client/.codex/SKILL.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/cross-client/.cursor/rules/ctx-audit.mdc.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/cross-client/AGENTS.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/hooks/session-stop-reminder.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/install.sh.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

ctx-plugin/skills/context-hygiene.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

get_comments.js.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0

specs/thread-context-doctor-spec.md.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2025 Knitli Inc. <knitli@knit.li>
+
+SPDX-License-Identifier: MIT OR Apache-2.0