codebase-memory-mcp/internal/cbm/cbm.c

#include "cbm.h"
#include "arena.h" // CBMArena, cbm_arena_init/alloc/strdup/destroy
#include "helpers.h"
#include "lang_specs.h"
#include "extract_unified.h"
#include "lsp/go_lsp.h"
#include "lsp/c_lsp.h"
#include "lsp/php_lsp.h"
#include "lsp/py_lsp.h"
#include "lsp/ts_lsp.h"
#include "lsp/cs_lsp.h"
#include "lsp/java_lsp.h"
#include "lsp/kotlin_lsp.h"
#include "lsp/rust_lsp.h"
#include "preprocessor.h"
#include "foundation/compat.h"
#include "foundation/compat_fs.h"  // cbm_fopen — crash-supervisor per-file marker write
#include "foundation/hash_table.h" // CBMHashTable — crash-supervisor quarantine set
#include "tree_sitter/api.h" // TSParser, TSNode, TSTree, TSInput, TSLanguage, TSPoint, TSParseOptions, TSParseState
#include "foundation/constants.h"
#include "mimalloc.h" // mi_malloc/mi_calloc/mi_realloc/mi_free/mi_usable_size — bind 3rd-party allocators (#424)
#if defined(CBM_BIND_TS_ALLOCATOR) && CBM_BIND_TS_ALLOCATOR
#include "sqlite3.h" // sqlite3_mem_methods, sqlite3_config, SQLITE_CONFIG_MALLOC — bind sqlite to mimalloc
#if defined(HAVE_LIBGIT2)
#include <git2/version.h>
#if defined(LIBGIT2_VERSION_CHECK)
#if !LIBGIT2_VERSION_CHECK(1, 7, 0)
#error "HAVE_LIBGIT2 requires libgit2 >= 1.7.0 for git_allocator"
#endif
#elif defined(LIBGIT2_VER_MAJOR) && defined(LIBGIT2_VER_MINOR) && defined(LIBGIT2_VER_REVISION)
#if ((LIBGIT2_VER_MAJOR * 1000000) + (LIBGIT2_VER_MINOR * 10000) + (LIBGIT2_VER_REVISION * 100)) < \
    1070000
#error "HAVE_LIBGIT2 requires libgit2 >= 1.7.0 for git_allocator"
#endif
#else
#error "HAVE_LIBGIT2 requires known libgit2 version macros for the >= 1.7.0 git_allocator guard"
#endif
#include <git2.h>           // git_libgit2_opts, GIT_OPT_SET_ALLOCATOR — bind libgit2 to mimalloc
#include <git2/sys/alloc.h> // git_allocator — not pulled in by <git2.h> (it's a sys/ header)
#endif
#endif
#include <stdint.h> // uint32_t, uint64_t, int64_t
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <time.h> // struct timespec, CLOCK_MONOTONIC

// Atomic counters for profiling parse vs extraction time (nanoseconds).
// Accessed from multiple threads; using _Atomic for safe accumulation.
#include <stdatomic.h>
static _Atomic uint64_t total_parse_ns = 0;
static _Atomic uint64_t total_extract_ns = 0;
static _Atomic uint64_t total_lsp_ns = 0;
static _Atomic uint64_t total_preprocess_ns = 0;
static _Atomic uint64_t total_files_preprocessed = 0;
static _Atomic uint64_t total_files = 0;

// C/C++ preprocessor #define macros are extracted as Macro nodes (#375). On a
// macro-dense codebase (e.g. the Linux kernel: ~2.4M macros, 49% of all nodes)
// this is the dominant extraction cost, so it is gated to the full/advanced
// index modes. Default ON to preserve behavior for direct callers/tests; the
// pipeline sets it from the index mode before extraction. Set once pre-extract,
// read-only during, so a relaxed atomic is sufficient.
static _Atomic int g_extract_macros = 1;
void cbm_set_macro_extraction(int enabled) {
    atomic_store_explicit(&g_extract_macros, enabled ? 1 : 0, memory_order_relaxed);
}
int cbm_macro_extraction_enabled(void) {
    return atomic_load_explicit(&g_extract_macros, memory_order_relaxed);
}

#define NSEC_PER_SEC 1000000000ULL
#define USEC_TO_NSEC 1000ULL
/* Use compat.h's cbm_clock_gettime which accepts CLOCK_MONOTONIC (value
 * varies by platform: 1 on Linux/Windows, 6 on macOS). We pass the
 * platform value via the compat.h fallback. */
#if defined(CLOCK_MONOTONIC)
#define CBM_CLOCK_MONO CLOCK_MONOTONIC
#elif defined(__APPLE__)
#define CBM_CLOCK_MONO 6
#else
#define CBM_CLOCK_MONO 1
#endif

static uint64_t now_ns(void) {
    struct timespec ts;
    cbm_clock_gettime(CBM_CLOCK_MONO, &ts);
    return ((uint64_t)ts.tv_sec * NSEC_PER_SEC) + (uint64_t)ts.tv_nsec;
}

// cbm_get_profile returns accumulated parse/extract times and file count.
void cbm_get_profile(cbm_profile_out_t out) {
    *out.parse_ns = atomic_load(&total_parse_ns);
    *out.extract_ns = atomic_load(&total_extract_ns);
    *out.files = atomic_load(&total_files);
}

uint64_t cbm_get_lsp_ns(void) {
    return atomic_load(&total_lsp_ns);
}

uint64_t cbm_get_preprocess_ns(void) {
    return atomic_load(&total_preprocess_ns);
}

uint64_t cbm_get_files_preprocessed(void) {
    return atomic_load(&total_files_preprocessed);
}

// cbm_reset_profile zeros the profiling counters.
void cbm_reset_profile(void) {
    atomic_store(&total_parse_ns, 0);
    atomic_store(&total_extract_ns, 0);
    atomic_store(&total_lsp_ns, 0);
    atomic_store(&total_preprocess_ns, 0);
    atomic_store(&total_files_preprocessed, 0);
    atomic_store(&total_files, 0);
}

// --- Growable array push functions ---

#define GROW_ARRAY(arr, arena)                                                                   \
    do {                                                                                         \
        if ((arr)->count >= (arr)->cap) {                                                        \
            int new_cap = (arr)->cap == 0 ? CBM_SZ_32 : (arr)->cap * PAIR_LEN;                   \
            void *new_items = cbm_arena_alloc((arena), (size_t)new_cap * sizeof(*(arr)->items)); \
            if (!new_items)                                                                      \
                return;                                                                          \
            if ((arr)->items && (arr)->count > 0) {                                              \
                memcpy(new_items, (arr)->items, (size_t)(arr)->count * sizeof(*(arr)->items));   \
            }                                                                                    \
            (arr)->items = new_items;                                                            \
            (arr)->cap = new_cap;                                                                \
        }                                                                                        \
    } while (0)

void cbm_defs_push(CBMDefArray *arr, CBMArena *a, CBMDefinition def) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = def;
}

void cbm_calls_push(CBMCallArray *arr, CBMArena *a, CBMCall call) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = call;
}

void cbm_imports_push(CBMImportArray *arr, CBMArena *a, CBMImport imp) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = imp;
}

void cbm_usages_push(CBMUsageArray *arr, CBMArena *a, CBMUsage usage) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = usage;
}

void cbm_throws_push(CBMThrowArray *arr, CBMArena *a, CBMThrow thr) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = thr;
}

void cbm_rw_push(CBMRWArray *arr, CBMArena *a, CBMReadWrite rw) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = rw;
}

void cbm_typerefs_push(CBMTypeRefArray *arr, CBMArena *a, CBMTypeRef tr) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = tr;
}

void cbm_envaccess_push(CBMEnvAccessArray *arr, CBMArena *a, CBMEnvAccess ea) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = ea;
}

void cbm_typeassign_push(CBMTypeAssignArray *arr, CBMArena *a, CBMTypeAssign ta) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = ta;
}

void cbm_stringref_push(CBMStringRefArray *arr, CBMArena *a, CBMStringRef sr) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = sr;
}

void cbm_infrabinding_push(CBMInfraBindingArray *arr, CBMArena *a, CBMInfraBinding ib) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = ib;
}

void cbm_impltrait_push(CBMImplTraitArray *arr, CBMArena *a, CBMImplTrait it) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = it;
}

void cbm_resolvedcall_push(CBMResolvedCallArray *arr, CBMArena *a, CBMResolvedCall rc) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = rc;
}

void cbm_channels_push(CBMChannelArray *arr, CBMArena *a, CBMChannel ch) {
    GROW_ARRAY(arr, a);
    arr->items[arr->count++] = ch;
}

// --- String input reader (for parse_with_options) ---

typedef struct {
    const char *string;
    uint32_t length;
} CBMStringInput;

static const char *cbm_string_read(void *payload, uint32_t byte, TSPoint point,
                                   uint32_t *bytes_read) {
    (void)point;
    CBMStringInput *self = (CBMStringInput *)payload;
    if (byte >= self->length) {
        *bytes_read = 0;
        return "";
    }
    *bytes_read = self->length - byte;
    return self->string + byte;
}

// --- Parse timeout callback ---

static bool cbm_timeout_cb(TSParseState *state) {
    uint64_t deadline = *(uint64_t *)state->payload;
    return now_ns() > deadline;
}

// --- Thread-local parser pool ---
// TSParser is not thread-safe, but can be reused across files on the same thread.
// We keep one parser per thread, and just switch language as needed.
// This avoids ~70K ts_parser_new()/ts_parser_delete() cycles on large repos.

static CBM_TLS TSParser *tl_parser = NULL;
static CBM_TLS CBMLanguage tl_parser_lang = CBM_LANG_COUNT; // invalid sentinel

// Get or create a thread-local parser configured for the given language.
static TSParser *get_thread_parser(const TSLanguage *ts_lang, CBMLanguage lang) {
    if (!tl_parser) {
        tl_parser = ts_parser_new();
        if (!tl_parser) {
            return NULL;
        }
        tl_parser_lang = CBM_LANG_COUNT;
    }
    if (tl_parser_lang != lang) {
        ts_parser_set_language(tl_parser, ts_lang);
        tl_parser_lang = lang;
    }
    return tl_parser;
}

// --- Allocator binding (defense-in-depth, #424) ---

/* Bind tree-sitter, sqlite3, and libgit2 to mimalloc explicitly so a correct
 * binary does NOT depend on the fragile MI_OVERRIDE symbol override. Under
 * MI_OVERRIDE=1 — particularly the Windows static-MinGW link with
 * --allow-multiple-definition — `malloc`/`free` can resolve to DIFFERENT
 * allocators (mimalloc vs the CRT) inside third-party libs, so a block
 * allocated by mimalloc gets freed by the CRT (or vice-versa), corrupting the
 * heap freelist (#424). Binding each library through one explicit allocator
 * eliminates that mismatch class generically, on every platform.
 *
 * Guarded to the production build (CBM_BIND_TS_ALLOCATOR=1, which CFLAGS_PROD
 * defines alongside MI_OVERRIDE=1). The test build is CRT + ASan, where binding
 * to mimalloc would mismatch ASan/CRT frees — there these binds compile to
 * no-ops and the build stays unchanged. */

#if defined(CBM_BIND_TS_ALLOCATOR) && CBM_BIND_TS_ALLOCATOR
#include <assert.h>

/* sqlite3 mem methods backed by mimalloc. sqlite's xMalloc/xRealloc/xSize use
 * `int` sizes; wrap with size_t casts. xRoundup rounds to an 8-byte boundary
 * (sqlite requires 8-byte-aligned roundup, and mimalloc honors that alignment).
 * Field order matches struct sqlite3_mem_methods exactly:
 * xMalloc, xFree, xRealloc, xSize, xRoundup, xInit, xShutdown, pAppData. */
static void *cbm_sqlite_malloc(int n) {
    return mi_malloc((size_t)n);
}
static void cbm_sqlite_free(void *p) {
    mi_free(p);
}
static void *cbm_sqlite_realloc(void *p, int n) {
    return mi_realloc(p, (size_t)n);
}
static int cbm_sqlite_size(void *p) {
    return (int)mi_usable_size(p);
}
static int cbm_sqlite_roundup(int n) {
    return (n + 7) & ~7; /* round up to 8-byte boundary */
}
static int cbm_sqlite_meminit(void *appdata) {
    (void)appdata;
    return SQLITE_OK;
}
static void cbm_sqlite_memshutdown(void *appdata) {
    (void)appdata;
}

#if defined(HAVE_LIBGIT2)
/* libgit2 >= 1.7 git_allocator backed by mimalloc. The struct has exactly
 * three members: gmalloc(size_t,file,line), grealloc(ptr,size,file,line),
 * gfree(ptr). The file/line args are ignored. */
static void *cbm_git_malloc(size_t n, const char *file, int line) {
    (void)file;
    (void)line;
    return mi_malloc(n);
}
static void *cbm_git_realloc(void *ptr, size_t size, const char *file, int line) {
    (void)file;
    (void)line;
    return mi_realloc(ptr, size);
}
static void cbm_git_free(void *ptr) {
    mi_free(ptr);
}
#endif /* HAVE_LIBGIT2 */
#endif /* CBM_BIND_TS_ALLOCATOR */

void cbm_alloc_init(void) {
#if defined(CBM_BIND_TS_ALLOCATOR) && CBM_BIND_TS_ALLOCATOR
    static int alloc_bound = 0; /* single-threaded startup; plain int is fine */
    if (alloc_bound) {
        return;
    }
    alloc_bound = 1;

    /* tree-sitter runtime (was previously bound in cbm_init; consolidated here). */
    ts_set_allocator(mi_malloc, mi_calloc, mi_realloc, mi_free);

    /* sqlite3. SQLITE_CONFIG_MALLOC MUST run before sqlite3_initialize / the
     * first sqlite3_open* — otherwise sqlite3_config returns SQLITE_MISUSE
     * silently and the binding is ignored. cbm_alloc_init() runs as the very
     * first statement of main(), before cbm_mcp_server_new → cbm_store_open*. */
    static sqlite3_mem_methods cbm_sqlite_mem = {
        cbm_sqlite_malloc,      /* xMalloc */
        cbm_sqlite_free,        /* xFree */
        cbm_sqlite_realloc,     /* xRealloc */
        cbm_sqlite_size,        /* xSize */
        cbm_sqlite_roundup,     /* xRoundup */
        cbm_sqlite_meminit,     /* xInit */
        cbm_sqlite_memshutdown, /* xShutdown */
        NULL,                   /* pAppData */
    };
    int sqlite_rc = sqlite3_config(SQLITE_CONFIG_MALLOC, &cbm_sqlite_mem);
    assert(sqlite_rc == SQLITE_OK && "SQLITE_CONFIG_MALLOC must run before sqlite3_initialize");
    (void)sqlite_rc;

#if defined(HAVE_LIBGIT2)
    /* libgit2. GIT_OPT_SET_ALLOCATOR MUST be set BEFORE git_libgit2_init():
     * libgit2's git_allocator_global_init (run during init) installs the default
     * stdalloc only if no custom allocator is set yet
     * (`if (git__allocator.gmalloc != git_failalloc_malloc) return 0;`), and the
     * pre-init global is the fail-allocator. There is no allocator-reset on
     * git_libgit2_shutdown, so binding once here — before pass_githistory's
     * per-call git_libgit2_init/shutdown pairs ever run — persists for the whole
     * process. git_libgit2_opts(GIT_OPT_SET_ALLOCATOR,...) itself does not
     * allocate, so calling it before init is safe. */
    static git_allocator cbm_git_alloc = {
        cbm_git_malloc,  /* gmalloc */
        cbm_git_realloc, /* grealloc */
        cbm_git_free,    /* gfree */
    };
    git_libgit2_opts(GIT_OPT_SET_ALLOCATOR, &cbm_git_alloc);
#endif /* HAVE_LIBGIT2 */
#endif /* CBM_BIND_TS_ALLOCATOR */
}

// --- Init/Shutdown ---

static int cbm_initialized = 0;

int cbm_init(void) {
    if (cbm_initialized) {
        return 0;
    }
    enum { CBM_INIT_DONE = 1 };
    cbm_initialized = CBM_INIT_DONE;
    /* Defense-in-depth allocator binds (idempotent). main() calls cbm_alloc_init
     * first; this covers non-main entry points (pipeline passes call cbm_init).
     * For sqlite the SQLITE_CONFIG_MALLOC bind only takes effect if it runs
     * before sqlite initializes — main() guarantees that ordering; here it is a
     * best-effort idempotent re-assert for paths that never hit main(). */
    cbm_alloc_init();
    return 0;
}

void cbm_reset_thread_parser(void) {
    // Release parser's internal slab-allocated subtrees (stack, cached token).
    // Must be called BEFORE cbm_slab_reset_thread() to avoid corrupting
    // live slab chunks that the parser still references.
    if (tl_parser) {
        ts_parser_reset(tl_parser);
    }
}

void cbm_destroy_thread_parser(void) {
    // Full cleanup: delete the parser. Call on worker thread exit.
    if (tl_parser) {
        ts_parser_delete(tl_parser);
        tl_parser = NULL;
        tl_parser_lang = CBM_LANG_COUNT;
    }
}

void cbm_shutdown(void) {
    // Clean up thread-local parser for the calling thread.
    // Note: other threads' TLS parsers are freed when those threads exit.
    cbm_destroy_thread_parser();
    cbm_initialized = 0;
}

// --- Bottleneck call-name classification (language-agnostic heuristics) ---

// Case-insensitive equality for short callee names.
static bool name_ieq(const char *a, const char *b) {
    for (; *a && *b; a++, b++) {
        if (tolower((unsigned char)*a) != tolower((unsigned char)*b)) {
            return false;
        }
    }
    return *a == '\0' && *b == '\0';
}

static bool name_in_set(const char *name, const char *const *set) {
    for (const char *const *s = set; *s; s++) {
        if (name_ieq(name, *s)) {
            return true;
        }
    }
    return false;
}

// Linear-scan / membership calls: a hit inside a loop is the textbook hidden
// O(n^2) (cf. Olivo et al., PLDI'15) that syntactic loop-depth alone misses.
static bool is_linear_scan_name(const char *n) {
    static const char *const set[] = {"find",    "indexof",   "contains", "includes", "search",
                                      "lookup",  "strstr",    "strchr",   "strrchr",  "memchr",
                                      "find_if", "findindex", "count",    "index",    NULL};
    return name_in_set(n, set);
}

// Allocation / growable-append calls: repeated inside a loop is the classic
// accidental reallocation / string-concat O(n^2). Names are deliberately
// conservative; meaningless in some languages → simply never matches there.
static bool is_alloc_name(const char *n) {
    static const char *const set[] = {"malloc",  "calloc",    "realloc",      "strdup", "strndup",
                                      "append",  "push_back", "emplace_back", "concat", "strcat",
                                      "strncat", "push",      "pushback",     NULL};
    return name_in_set(n, set);
}

// Extract the receiver identifier from a def's receiver text — Go's
// "(s *Store)" / "(s Store)" → "s". Stores the identifier start in *out and
// returns its length; returns 0 for unnamed receivers ("(*Store)", "(Store)"),
// where no second token follows the identifier (a lone token is the TYPE, not
// a name — such methods have no receiver variable to call through anyway).
static size_t receiver_ident(const char *recv_text, const char **out) {
    const char *p = recv_text;
    if (*p == '(') {
        p++;
    }
    while (*p == ' ' || *p == '\t') {
        p++;
    }
    const char *start = p;
    while ((*p >= 'a' && *p <= 'z') || (*p >= 'A' && *p <= 'Z') || (*p >= '0' && *p <= '9') ||
           *p == '_') {
        p++;
    }
    size_t len = (size_t)(p - start);
    if (len == 0) {
        return 0; // "(*Store)": leading '*', no identifier
    }
    while (*p == ' ' || *p == '\t') {
        p++;
    }
    if (*p == ')' || *p == '\0') {
        return 0; // "(Store)": single token is the type, receiver unnamed
    }
    *out = start;
    return len;
}

// Whether a callee expression targets the same instance/class as the enclosing
// def, i.e. counts as genuine self-recursion rather than a same-named call on a
// different receiver. callee_name may be bare ("recur") or qualified
// ("self.recur", "this.recur", "super().save", "axios.get", "self.obj.recur").
//
// Bare names have no receiver → assume self-call (free function calling itself
// by bare name; preserves prior behavior). Qualified names: the receiver chain
// is everything before the LAST '.', and the WHOLE chain must name the same
// object — self/this/cls/@self, or the enclosing def's own receiver identifier
// (Go: `s` in `func (s *Store) save()`, from CBMDefinition.receiver). Matching
// the whole chain (not its first segment) keeps self.obj.recur() out: it
// targets self's FIELD obj, a different object. super() is the parent class and
// any other receiver (axios, console, ...) a different target. See #599.
static bool is_self_receiver(const char *callee_name, const char *def_receiver) {
    if (!callee_name || !callee_name[0]) {
        return false;
    }
    const char *dot = strrchr(callee_name, '.');
    if (!dot) {
        return true; // bare name → self-recursion candidate
    }
    size_t rlen = (size_t)(dot - callee_name);
    static const char *const self_receivers[] = {"self", "this", "cls", "@self", NULL};
    for (int i = 0; self_receivers[i]; i++) {
        size_t sl = strlen(self_receivers[i]);
        if (rlen == sl && strncmp(callee_name, self_receivers[i], sl) == 0) {
            return true;
        }
    }
    if (def_receiver) {
        const char *rid = NULL;
        size_t ril = receiver_ident(def_receiver, &rid);
        if (ril > 0 && ril == rlen && strncmp(callee_name, rid, ril) == 0) {
            return true; // call through the enclosing method's own receiver
        }
    }
    return false; // super() / axios / console / self.obj / any other receiver
}

// Count parameters from a signature string like "(int a, Foo* b, cb (*)(int,int))".
// Fallback for languages where param_names isn't populated (e.g. C keeps only the
// signature text). Counts commas at the top paren level; treats "()"/"(void)" as 0.
// Approximate by design (a structural smell, not an exact arity).
static int count_params_from_signature(const char *sig) {
    if (!sig) {
        return 0;
    }
    const char *p = sig;
    while (*p && *p != '(') {
        p++;
    }
    if (*p != '(') {
        return 0;
    }
    p++;
    const char *list = p;
    int depth = 0;
    int commas = 0;
    bool any = false;
    for (; *p; p++) {
        char ch = *p;
        if (ch == '(' || ch == '[' || ch == '{' || ch == '<') {
            depth++;
        } else if (ch == ')') {
            if (depth == 0) {
                break;
            }
            depth--;
        } else if (ch == ']' || ch == '}' || ch == '>') {
            if (depth > 0) {
                depth--;
            }
        } else if (ch == ',' && depth == 0) {
            commas++;
        } else if (!isspace((unsigned char)ch)) {
            any = true;
        }
    }
    if (!any) {
        return 0; /* "()" */
    }
    if (commas == 0) {
        while (*list == ' ' || *list == '\t') {
            list++;
        }
        if (strncmp(list, "void", 4) == 0 &&
            (list[4] == ')' || list[4] == ' ' || list[4] == '\0')) {
            return 0; /* C "(void)" */
        }
    }
    return commas + 1;
}

// --- Main extraction function ---

/* Test-only deterministic fault injection for the crash/hang supervisor tests.
 * Gated entirely behind env vars that are never set in production; a matching
 * rel_path either aborts (a fault signal the supervisor classifies as a crash)
 * or spins forever (an external-scanner infinite loop the quiet-timeout kills).
 * This gives an honest guard — green iff the supervisor actually contains a real
 * fault — instead of a fixture that may stop faulting once a root cause is fixed. */
/* Crash-supervisor per-file marker (Stage 3c skip-and-continue). In the
 * supervisor's single-threaded recovery re-run, cbm_extract_file records the
 * file it is ABOUT to process here (CBM_INDEX_MARKER_FILE) before touching it,
 * so that if this file hard-crashes the worker the parent can read the marker
 * back and learn the EXACT crasher to quarantine. Only meaningful single-
 * threaded (parallel would race the marker); the env var is set solely by the
 * supervisor during recovery, so it is a no-op on every normal run. */
static void cbm_index_write_marker(const char *rel_path) {
    const char *mf = getenv("CBM_INDEX_MARKER_FILE");
    if (!mf || !mf[0] || !rel_path || !rel_path[0]) {
        return;
    }
    FILE *f = cbm_fopen(mf, "wb");
    if (f) {
        (void)fputs(rel_path, f);
        (void)fclose(f);
    }
}

/* ── Crash-quarantine set (Stage 3c skip-and-continue) ──────────────────────
 * After a crash the supervisor re-runs the worker single-threaded, passing
 * CBM_INDEX_QUARANTINE_FILE — a newline-delimited list of repo-relative paths
 * that already crashed the indexer and MUST NOT be extracted again. Owned here,
 * next to the other env-driven extract hooks (marker + fault injector), so the
 * single hard guard lives at the one choke point every pass funnels through
 * (cbm_extract_file): whether a pass re-extracts from disk on a cache miss
 * (sequential pass_calls/usages/semantic) or extracts fresh, a quarantined file
 * short-circuits to an empty result and never reaches the parser/crash. The
 * pipeline extract loops separately REPORT the skip as phase="crash" via
 * cbm_index_is_quarantined() so the crasher surfaces in the response skipped[].
 * Loaded once, lazily; read-only after load (safe for the parallel workers,
 * though recovery runs single-threaded). Unset env ⇒ empty set ⇒ cheap no-op. */
static CBMHashTable *g_quarantine_set = NULL;
enum { CBM_QSET_UNINIT = 0, CBM_QSET_INITING = 1, CBM_QSET_INITED = 2 };
static atomic_int g_quarantine_state = CBM_QSET_UNINIT;

static void cbm_quarantine_load(void) {
    const char *qf = getenv("CBM_INDEX_QUARANTINE_FILE");
    if (!qf || !qf[0]) {
        return; /* normal path: empty set */
    }
    FILE *f = cbm_fopen(qf, "rb");
    if (!f) {
        return;
    }
    CBMHashTable *set = cbm_ht_create(16);
    if (!set) {
        (void)fclose(f);
        return;
    }
    char line[2048];
    while (fgets(line, sizeof(line), f)) {
        size_t len = strlen(line);
        while (len > 0 && (line[len - 1] == '\n' || line[len - 1] == '\r')) {
            line[--len] = '\0';
        }
        if (len == 0) {
            continue;
        }
        /* Line format: "path\tphase" where phase is "crash" or "hang". A bare
         * "path" line (no tab) is tolerated and defaults to phase "crash" for
         * backward compatibility with older quarantine files. */
        char *tab = strchr(line, '\t');
        const char *phase = "crash";
        if (tab) {
            *tab = '\0';
            if (tab[1]) {
                phase = tab + 1;
            }
        }
        if (line[0] == '\0') {
            continue; /* empty path (line began with a tab) — skip */
        }
        /* The table borrows the key + value pointers, so dup both. Intentionally
         * never freed: the set lives for the whole (short-lived worker) process.
         * The value stores the phase so cbm_index_quarantine_phase() can report
         * "crash" vs "hang"; membership (cbm_index_is_quarantined) is value != NULL. */
        char *key = cbm_strdup(line);
        char *pval = cbm_strdup(phase);
        if (key && pval) {
            cbm_ht_set(set, key, (void *)pval);
        }
    }
    (void)fclose(f);
    g_quarantine_set = set;
}

bool cbm_index_is_quarantined(const char *rel_path) {
    if (!rel_path || !rel_path[0]) {
        return false;
    }
    int state = atomic_load(&g_quarantine_state);
    if (state != CBM_QSET_INITED) {
        /* First caller wins the CAS and loads; racers spin until INITED.
         * Same once-init pattern as cbm_ui_log_init (http_server.c). */
        state = CBM_QSET_UNINIT;
        if (atomic_compare_exchange_strong(&g_quarantine_state, &state, CBM_QSET_INITING)) {
            cbm_quarantine_load();
            atomic_store(&g_quarantine_state, CBM_QSET_INITED);
        } else {
            while (atomic_load(&g_quarantine_state) != CBM_QSET_INITED) {
                cbm_usleep(1000); /* 1ms */
            }
        }
    }
    return g_quarantine_set && cbm_ht_has(g_quarantine_set, rel_path);
}

const char *cbm_index_quarantine_phase(const char *rel_path) {
    /* cbm_index_is_quarantined drives the lazy once-load and returns true only
     * when the set is loaded and holds rel_path — so on true, g_quarantine_set is
     * non-NULL and the stored value is the phase string ("crash"/"hang"). */
    if (!cbm_index_is_quarantined(rel_path)) {
        return NULL;
    }
    return (const char *)cbm_ht_get(g_quarantine_set, rel_path);
}

static void cbm_test_fault_inject(const char *rel_path) {
    if (!rel_path || !rel_path[0]) {
        return;
    }
    const char *crash_on = getenv("CBM_TEST_CRASH_ON");
    if (crash_on && crash_on[0] && strstr(rel_path, crash_on)) {
        abort(); /* SIGABRT → WIFSIGNALED → classified as a crash */
    }
    const char *hang_on = getenv("CBM_TEST_HANG_ON");
    if (hang_on && hang_on[0] && strstr(rel_path, hang_on)) {
        for (;;) {
            /* Busy-spin: the supervisor's quiet-timeout kills + reports us. */
        }
    }
}

CBMFileResult *cbm_extract_file(const char *source, int source_len, CBMLanguage language,
                                const char *project, const char *rel_path, int64_t timeout_micros,
                                const char **extra_defines, const char **include_paths) {
    // Allocate result on heap (arena inside for all string data)
    enum { SINGLE = 1 };
    CBMFileResult *result = (CBMFileResult *)calloc(SINGLE, sizeof(CBMFileResult));
    if (!result) {
        return NULL;
    }

    cbm_arena_init(&result->arena);
    CBMArena *a = &result->arena;

    /* Crash-quarantine hard guard (Stage 3c): a file the supervisor pinned as a
     * crasher must NEVER be parsed again. Return a clean empty result BEFORE the
     * marker write and fault injector so no pass (including sequential re-extract
     * passes that miss the result cache) can crash on it. The pipeline extract
     * loops separately record it as a phase="crash" skip. Checked before the
     * marker so quarantined files never overwrite it — the marker keeps pointing
     * at the real (non-quarantined) file being processed when a crash hits. */
    if (cbm_index_is_quarantined(rel_path)) {
        return result;
    }

    cbm_index_write_marker(rel_path);
    cbm_test_fault_inject(rel_path);

    // Get language spec
    const CBMLangSpec *spec = cbm_lang_spec(language);
    if (!spec) {
        result->has_error = true;
        result->error_msg = cbm_arena_strdup(a, "unsupported language");
        return result;
    }

    // Get tree-sitter language
    const TSLanguage *ts_lang = cbm_ts_language(language);
    if (!ts_lang) {
        result->has_error = true;
        result->error_msg = cbm_arena_strdup(a, "no tree-sitter grammar");
        return result;
    }

    // Get thread-local parser (reused across files on same thread)
    TSParser *parser = get_thread_parser(ts_lang, language);
    if (!parser) {
        result->has_error = true;
        result->error_msg = cbm_arena_strdup(a, "parser alloc failed");
        return result;
    }

    // Reset parser state from any previous parse (cancellation flags etc.)
    ts_parser_reset(parser);

    uint64_t t0 = now_ns();

    // Build string input + timeout options for parse_with_options
    CBMStringInput str_input = {source, (uint32_t)source_len};
    TSInput ts_input = {
        &str_input,
        cbm_string_read,
        TSInputEncodingUTF8,
        NULL,
    };

    TSParseOptions opts = {0};
    uint64_t deadline_ns = 0; // cppcheck-suppress unreadVariable
    if (timeout_micros > 0) {
        deadline_ns = t0 + ((uint64_t)timeout_micros * USEC_TO_NSEC);
        opts.payload = &deadline_ns;
        opts.progress_callback = cbm_timeout_cb;
    }

    TSTree *tree = ts_parser_parse_with_options(parser, NULL, ts_input, opts);
    uint64_t t1 = now_ns();

    if (!tree) {
        result->has_error = true;
        result->error_msg =
            cbm_arena_strdup(a, timeout_micros > 0 ? "parse timeout" : "parse failed");
        return result;
    }

    TSNode root = ts_tree_root_node(tree);

    // Compute module QN. Java/Go derive the module from the CONTAINING
    // DIRECTORY (package semantics) rather than baking the filename stem in,
    // so def QNs, the LSP caller_qn, and the textual calls-enclosing QN all
    // agree (e.g. Outer.java -> module "proj", not "proj.Outer"). Other
    // languages are unchanged.
    result->module_qn = cbm_fqn_module_source_lang(a, project, rel_path, language);
    result->is_test_file = cbm_is_test_file(rel_path, language);

    // Build extraction context
    CBMExtractCtx ctx = {
        .arena = a,
        .result = result,
        .source = source,
        .source_len = source_len,
        .language = language,
        .project = project,
        .rel_path = rel_path,
        .module_qn = result->module_qn,
        .root = root,
    };

    // Run extractors: defs + imports use separate walks (unique recursion patterns),
    // then a single unified cursor walk handles the remaining 7 extractors.
    cbm_extract_definitions(&ctx);
    cbm_extract_imports(&ctx);
    cbm_extract_unified(&ctx);

    // Channel detection (Socket.IO / EventEmitter) — JS/TS only.
    cbm_extract_channels(&ctx);

    // K8s / Kustomize semantic pass (additional structured extraction for YAML-based infra files).
    if (ctx.language == CBM_LANG_KUSTOMIZE || ctx.language == CBM_LANG_K8S) {
        cbm_extract_k8s(&ctx);
    }

    // LSP type-aware call/usage resolution (per-file). Runs in every mode;
    // refines the tree-sitter + textual-resolution graph with type info.
    uint64_t lsp_start = now_ns();
    {
        if (language == CBM_LANG_GO) {
            cbm_run_go_lsp(a, result, source, source_len, root);
        }
        if (language == CBM_LANG_C || language == CBM_LANG_CPP || language == CBM_LANG_CUDA) {
            cbm_run_c_lsp(a, result, source, source_len, root, language != CBM_LANG_C);
        }
        if (language == CBM_LANG_PHP) {
            cbm_run_php_lsp(a, result, source, source_len, root);
        }
        if (language == CBM_LANG_PYTHON) {
            cbm_run_py_lsp(a, result, source, source_len, root);
        }
        if (language == CBM_LANG_JAVASCRIPT || language == CBM_LANG_TYPESCRIPT ||
            language == CBM_LANG_TSX) {
            bool js_mode = (language == CBM_LANG_JAVASCRIPT);
            // jsx_mode: TSX always; .jsx in the JS bucket also enables it.
            bool jsx_mode = (language == CBM_LANG_TSX);
            if (language == CBM_LANG_JAVASCRIPT && rel_path) {
                size_t rl = strlen(rel_path);
                if (rl >= 4 && strcmp(rel_path + rl - 4, ".jsx") == 0)
                    jsx_mode = true;
            }
            // dts_mode: ".d.ts" suffix (TypeScript only).
            bool dts_mode = false;
            if (language == CBM_LANG_TYPESCRIPT && rel_path) {
                size_t rl = strlen(rel_path);
                if (rl >= 5 && strcmp(rel_path + rl - 5, ".d.ts") == 0)
                    dts_mode = true;
            }
            cbm_run_ts_lsp(a, result, source, source_len, root, js_mode, jsx_mode, dts_mode);
        }
        if (language == CBM_LANG_CSHARP) {
            cbm_run_cs_lsp(a, result, source, source_len, root);
        }
    }
    if (language == CBM_LANG_JAVA) {
        cbm_run_java_lsp(a, result, source, source_len, root);
    }
    if (language == CBM_LANG_KOTLIN) {
        cbm_run_kotlin_lsp(a, result, source, source_len, root);
    }
    if (language == CBM_LANG_RUST) {
        cbm_run_rust_lsp(a, result, source, source_len, root);
    }
    atomic_fetch_add(&total_lsp_ns, now_ns() - lsp_start);

    // Calls extracted so far all carry ORIGINAL-source line numbers; the C/C++
    // preprocessor second pass below appends calls with EXPANDED-source lines,
    // which must not be used for the def line-range attribution of the bottleneck
    // metrics. Remember the boundary.
    int orig_calls_count = result->calls.count;

    // Second pass: preprocess C/C++/CUDA and extract additional macro-hidden calls.
    // Defs keep original-source line numbers; only CALLS are extracted from expanded source.
    if (language == CBM_LANG_C || language == CBM_LANG_CPP || language == CBM_LANG_CUDA) {
        uint64_t pp_start = now_ns();
        char *expanded = cbm_preprocess(source, source_len, rel_path, extra_defines, include_paths,
                                        language != CBM_LANG_C);
        if (expanded) {
            int expanded_len = (int)strlen(expanded);
            // Record calls count before second pass
            int calls_before = result->calls.count;

            // Parse expanded source with fresh tree
            TSParser *pp_parser = get_thread_parser(ts_lang, language);
            if (pp_parser) {
                ts_parser_reset(pp_parser);
                CBMStringInput pp_input = {expanded, (uint32_t)expanded_len};
                TSInput pp_ts_input = {
                    &pp_input,
                    cbm_string_read,
                    TSInputEncodingUTF8,
                    NULL,
                };
                TSParseOptions pp_opts = {0};
                TSTree *pp_tree =
                    ts_parser_parse_with_options(pp_parser, NULL, pp_ts_input, pp_opts);
                if (pp_tree) {
                    TSNode pp_root = ts_tree_root_node(pp_tree);

                    // Build context for expanded source — extract only calls via unified extractor
                    CBMExtractCtx pp_ctx = {
                        .arena = a,
                        .result = result,
                        .source = expanded,
                        .source_len = expanded_len,
                        .language = language,
                        .project = project,
                        .rel_path = rel_path,
                        .module_qn = result->module_qn,
                        .root = pp_root,
                    };
                    // Re-run unified extraction on expanded source.
                    // This adds macro-expanded calls; duplicates with original calls are
                    // harmless (pipeline deduplicates by caller+callee).
                    cbm_extract_unified(&pp_ctx);

                    // Also run LSP on expanded source for additional type-resolved
                    // calls (language is already C/C++/CUDA — checked in enclosing
                    // block). Runs in every mode.
                    cbm_run_c_lsp(a, result, expanded, expanded_len, pp_root,
                                  language != CBM_LANG_C);

                    ts_tree_delete(pp_tree);
                }
            }
            cbm_preprocess_free(expanded);
            atomic_fetch_add(&total_files_preprocessed, 1);
            (void)calls_before; // used for future logging
        }
        atomic_fetch_add(&total_preprocess_ns, now_ns() - pp_start);
    }

    // Bottleneck call-context metrics. Each call is attributed to the INNERMOST
    // enclosing Function/Method def by source-line range (defs and calls in one
    // CBMFileResult share the same file). Range matching is used instead of
    // enclosing_func_qn string matching because some grammars (notably C, whose
    // function_definition has no "name" field) attribute the call's scope to the
    // module rather than the function — line ranges are unambiguous and
    // language-agnostic. Bounded per file (defs x calls), not a repo-scale scan.
    int def_count = result->defs.count;
    bool *has_self = def_count > 0 ? calloc((size_t)def_count, sizeof(bool)) : NULL;
    bool *has_guarded = def_count > 0 ? calloc((size_t)def_count, sizeof(bool)) : NULL;

    // param_count is a standalone structural smell (independent of calls). Prefer
    // the parsed param_names array; fall back to counting from the signature text
    // for languages (e.g. C) that populate only the signature.
    for (int di = 0; di < def_count; di++) {
        CBMDefinition *d = &result->defs.items[di];
        int pc = 0;
        if (d->param_names) {
            while (d->param_names[pc]) {
                pc++;
            }
        }
        if (pc == 0 && d->signature) {
            pc = count_params_from_signature(d->signature);
        }
        d->param_count = pc;
    }

    for (int ci = 0; ci < orig_calls_count; ci++) {
        const CBMCall *c = &result->calls.items[ci];
        if (!c->callee_name || c->start_line <= 0) {
            continue;
        }
        // Innermost enclosing Function/Method def by line range (smallest span).
        int best = -1;
        int best_span = -1;
        for (int di = 0; di < def_count; di++) {
            const CBMDefinition *d = &result->defs.items[di];
            if (!d->name || !d->label ||
                (strcmp(d->label, "Function") != 0 && strcmp(d->label, "Method") != 0)) {
                continue;
            }
            if ((int)d->start_line <= c->start_line && c->start_line <= (int)d->end_line) {
                int span = (int)d->end_line - (int)d->start_line;
                if (best < 0 || span < best_span) {
                    best_span = span;
                    best = di;
                }
            }
        }
        if (best < 0) {
            continue;
        }
        CBMDefinition *d = &result->defs.items[best];
        // callee_name may be bare ("recur") or qualified ("self.recur",
        // "super().save", "axios.get"). A short-name match alone is not
        // self-recursion: the callee must also target the same object
        // (is_self_receiver), or super().save() inside save and axios.get
        // inside get are false positives (#599).
        const char *dot = strrchr(c->callee_name, '.');
        const char *callee_short = dot ? dot + 1 : c->callee_name;
        bool in_loop = c->loop_depth > 0;

        if (strcmp(callee_short, d->name) == 0 && is_self_receiver(c->callee_name, d->receiver)) {
            // Direct self-recursion. The call graph omits self-edges (pass_calls
            // skips source==target), so detect it here; seeds "recursive".
            d->is_recursive = true;
            if (has_self) {
                has_self[best] = true;
            }
            if (in_loop) {
                d->recursion_in_loop = true; // recursion compounded by a loop
            }
            if (c->branch_depth > 0 && has_guarded) {
                has_guarded[best] = true; // a self-call guarded by some conditional
            }
        }
        if (in_loop && is_linear_scan_name(callee_short)) {
            d->linear_scan_in_loop++; // hidden O(n^2): linear scan inside a loop
        }
        if (in_loop && is_alloc_name(callee_short)) {
            d->alloc_in_loop++; // repeated allocation/append inside a loop
        }
    }

    // Recursive with no self-call guarded by any conditional → no obvious base
    // case on the recursive path: a stronger "potentially unbounded" signal.
    for (int di = 0; di < def_count; di++) {
        if (has_self && has_self[di] && !(has_guarded && has_guarded[di])) {
            result->defs.items[di].unguarded_recursion = true;
        }
    }
    free(has_self);
    free(has_guarded);

    uint64_t t2 = now_ns();

    result->imports_count = result->imports.count;

    // Accumulate profiling counters
    atomic_fetch_add(&total_parse_ns, t1 - t0);
    atomic_fetch_add(&total_extract_ns, t2 - t1);
    atomic_fetch_add(&total_files, 1);

    // Retain tree for cross-file LSP reuse (caller frees via cbm_free_tree)
    result->cached_tree = tree;
    result->cached_lang = language;
    return result;
}

void cbm_free_result(CBMFileResult *result) {
    if (!result) {
        return;
    }
    if (result->cached_tree) {
        ts_tree_delete(result->cached_tree);
        result->cached_tree = NULL;
    }
    cbm_arena_destroy(&result->arena);
    free(result);
}

void cbm_free_tree(CBMFileResult *result) {
    if (result && result->cached_tree) {
        ts_tree_delete(result->cached_tree);
        result->cached_tree = NULL;
    }
}

void cbm_free_tree_ptr(TSTree *tree) {
    if (tree) {
        ts_tree_delete(tree);
    }
}