@@ -155,6 +155,8 @@ Watcher registration is controlled separately by `auto_watch` (default `true`).
 
 To turn the watcher off entirely, set `config set watcher_enabled false` (default `true`): the background poll thread never starts and no project is registered, while `auto_index` and manual `index_repository` keep working. Unlike `auto_watch` — which is consulted per session — `watcher_enabled` is read once when the background daemon starts, so run `codebase-memory-mcp daemon stop` after changing it; reconnecting your MCP client alone will not restart the daemon. See [docs/CONFIGURATION.md](docs/CONFIGURATION.md#2-cli-managed-runtime-settings).
 
+Linked git worktrees are indexed as their own projects by default. Set `config set ignore_worktrees true` to skip them on the automatic paths — useful when short-lived `git worktree add` checkouts would otherwise each leave behind a permanent index of the same repository. An explicit `index_repository` call on a worktree is then refused unless you pass `index_worktree=true`. See [docs/CONFIGURATION.md](docs/CONFIGURATION.md#ignore_worktrees).
+
 ### Keeping Up to Date
 
 **Updates run from the install script on every platform, not from inside the running binary.** `codebase-memory-mcp update` validates your flags and then prints the exact command to run:
@@ -735,6 +737,7 @@ codebase-memory-mcp config list                          # show all settings
 codebase-memory-mcp config set auto_index true           # auto-index on session start
 codebase-memory-mcp config set auto_index_limit 50000    # max files for auto-index
 codebase-memory-mcp config set auto_watch false          # don't register background git watcher (default: true)
+codebase-memory-mcp config set ignore_worktrees true     # skip linked git worktrees when auto-indexing (default: false)
 codebase-memory-mcp config set watcher_enabled false     # stop the watcher thread entirely (default: true)
 codebase-memory-mcp config set index_max_files 250000    # optional per-index source-file limit
 codebase-memory-mcp config set index_max_source_mb 16384 # optional per-index source-size limit
 
@@ -87,6 +87,7 @@ Current keys:
 |---|---|---|
 | `auto_index` | `false` | Automatically index new projects when an MCP session starts. |
 | `auto_index_limit` | `50000` | Maximum file count allowed for automatic indexing of a new project. |
+| `ignore_worktrees` | `false` | Skip linked git worktrees (`git worktree add`) when indexing automatically. |
 | `auto_watch` | `true` | Register the session's project with the background git watcher on connect. Set `false` to keep a session from registering its project (the watcher still runs for other projects). |
 | `watcher_enabled` | `true` | Master switch for the background watcher subsystem. Set `false` to stop the watcher from starting at all — no poll thread and no project registration. Reindex manually with `index_repository` when disabled. |
 | `index_max_files` | `off` | Optional maximum number of accepted source files in one discovery run. |
@@ -126,6 +127,35 @@ and preserves any previously serving database. See
 [Index resource limits](INDEX_RESOURCE_LIMITS.md) for counting, validation, and
 error-response details.
 
+### `ignore_worktrees`
+
+Every indexed project is registered under its own absolute root path, so each
+linked worktree becomes a separate permanent index. On machines that create many
+short-lived worktrees, the automatic paths (`auto_index`, and the session hook's
+"index this project first" guidance) turn every throwaway checkout into another
+stored index of what is largely the same repository.
+
+Enable the key to keep those checkouts out of the index:
+
+```bash
+codebase-memory-mcp config set ignore_worktrees true
+```
+
+With it enabled:
+
+- automatic indexing skips a session whose root is a linked worktree;
+- the `hook-augment` context says the worktree is unindexed on purpose instead
+  of telling the agent to run `index_repository`;
+- an explicit `index_repository` call on a linked worktree is refused, and names
+  both ways forward — pass `index_worktree=true` for that one call, or turn the
+  key back off.
+
+The main checkout of the same repository is unaffected, as are ordinary clones
+and submodules. Detection is git plumbing only: a linked worktree's `.git` is a
+file pointing at a gitdir that contains a `commondir` entry.
+
+The default is `false`, so indexing behavior is unchanged unless you opt in.
+
 ## 3. UI Settings
 
 The optional built-in graph UI stores its settings in:
 
@@ -7442,6 +7442,7 @@ static const config_key_def_t CONFIG_KEYS[] = {
     {CBM_CONFIG_AUTO_INDEX, "false", "Enable auto-indexing on MCP session start"},
     {CBM_CONFIG_AUTO_INDEX_LIMIT, "50000", "Max files for auto-indexing new projects"},
     {CBM_CONFIG_AUTO_WATCH, "true", "Register background git watcher on session connect"},
+    {CBM_CONFIG_IGNORE_WORKTREES, "false", "Skip linked git worktrees when indexing automatically"},
     {CBM_CONFIG_WATCHER_ENABLED, "true",
      "Run the background watcher thread (auto-reindex); false to disable"},
     {CBM_CONFIG_UI_LANG, "auto", "Pin graph UI language: en, zh, or auto"},
 
@@ -250,7 +250,8 @@ bool cbm_hook_augment_invocation_supported_for_testing(const char *dialect,
                                                        const char *forced_event);
 bool cbm_hook_path_contains_for_testing(const char *root, const char *candidate,
                                         bool case_insensitive);
-const char *cbm_hook_no_project_index_guidance_for_testing(const char *event);
+const char *cbm_hook_no_project_index_guidance_for_testing(const char *event,
+                                                           bool worktree_ignored);
 bool cbm_hook_augment_parse_bash_pattern_for_testing(const char *cmd, char *out, size_t out_sz);
 bool cbm_mcp_command_path_probe_safe_for_testing(const char *command, bool windows);
 void cbm_set_mcp_command_path_probe_counter_for_testing(int *counter);
@@ -431,6 +432,7 @@ bool cbm_config_load_index_policy(cbm_config_t *cfg, cbm_index_resource_policy_t
 #define CBM_CONFIG_AUTO_INDEX "auto_index"
 #define CBM_CONFIG_AUTO_INDEX_LIMIT "auto_index_limit"
 #define CBM_CONFIG_AUTO_WATCH "auto_watch"
+#define CBM_CONFIG_IGNORE_WORKTREES "ignore_worktrees"
 #define CBM_CONFIG_UI_LANG "ui-lang"
 #define CBM_CONFIG_WATCHER_ENABLED "watcher_enabled"
 /* #1558: the graph UI's loopback listener. Stored in the UI config file rather
 
@@ -21,7 +21,9 @@
 #include "foundation/constants.h"
 #include "foundation/mem.h"
 #include "foundation/platform.h"
+#include "git/git_context.h"
 #include "mcp/mcp.h"
+#include "mcp/mcp_internal.h"
 #include "pipeline/pipeline.h"
 #include "yyjson/yyjson.h"
 
@@ -1440,7 +1442,14 @@ static const char *ha_active_tier(yyjson_val *root, const char *event) {
     return "Tier 2 verification";
 }
 
-static const char *ha_no_project_index_guidance(const char *event) {
+static const char *ha_no_project_index_guidance(const char *event, bool worktree_ignored) {
+    /* ignore_worktrees is on and this cwd is a linked worktree: indexing it is
+     * deliberately disabled, so telling the agent to run index_repository would
+     * only produce a refusal. Point at the setting instead. */
+    if (worktree_ignored) {
+        return "This is a linked git worktree and ignore_worktrees is enabled, so it is not "
+               "indexed on purpose; do not run index_repository here.";
+    }
     return event && strcmp(event, "SubagentStart") == 0
                ? "Ask the parent agent to run index_repository before structural exploration; "
                  "do not attempt graph mutation."
@@ -1472,6 +1481,8 @@ static char *ha_lifecycle_json_from_root(cbm_mcp_server_t *srv, yyjson_val *root
     }
     const char *cwd = ha_normalized_cwd_with_server(root, srv, cwd_buffer, sizeof(cwd_buffer));
     char *project = srv && cwd ? ha_resolve_indexed_project(srv, cwd) : NULL;
+    bool worktree_ignored = !project && srv && cwd && cbm_mcp_ignore_worktrees_enabled(srv) &&
+                            cbm_git_is_linked_worktree(cwd);
     cbm_mcp_server_free(owned_server);
 
     char context[2048];
@@ -1505,7 +1516,7 @@ static char *ha_lifecycle_json_from_root(cbm_mcp_server_t *srv, yyjson_val *root
                  "and file reads for literals, configs, non-code files, and verification.",
                  scope, safe_project, tier);
     } else {
-        const char *index_guidance = ha_no_project_index_guidance(event);
+        const char *index_guidance = ha_no_project_index_guidance(event, worktree_ignored);
         snprintf(context, sizeof(context),
                  "[codebase-memory] %s context: no indexed graph project matched this working "
                  "directory. %s Once indexed, "
@@ -1624,8 +1635,9 @@ bool cbm_hook_path_contains_for_testing(const char *root, const char *candidate,
     return ha_path_contains_mode(root, candidate, case_insensitive);
 }
 
-const char *cbm_hook_no_project_index_guidance_for_testing(const char *event) {
-    return ha_no_project_index_guidance(event);
+const char *cbm_hook_no_project_index_guidance_for_testing(const char *event,
+                                                           bool worktree_ignored) {
+    return ha_no_project_index_guidance(event, worktree_ignored);
 }
 
 bool cbm_hook_augment_parse_bash_pattern_for_testing(const char *cmd, char *out, size_t out_sz) {
 
@@ -15,6 +15,7 @@
 #include "foundation/sha256.h"
 #include "foundation/subprocess.h"
 #include "foundation/workspace.h"
+#include "git/git_context.h"
 #include "mcp/index_supervisor.h"
 #include "mcp/mcp.h"
 #include "mcp/mcp_internal.h"
@@ -2071,6 +2072,11 @@ static void application_background_initialize_impl(cbm_daemon_application_sessio
         !application_session_workspace_allowed(session, "auto_index_discovery")) {
         auto_index_candidate = false;
     }
+    if (auto_index_candidate && cbm_mcp_ignore_worktrees_enabled(session->mcp) &&
+        cbm_git_is_linked_worktree(root_path)) {
+        cbm_log_info("daemon.autoindex.skipped", "project", project, "reason", "linked_worktree");
+        auto_index_candidate = false;
+    }
     bool within_auto_index_limit =
         !auto_index_candidate ||
         cbm_mcp_auto_index_within_file_limit(root_path, auto_index_limit, &tracked_files);
 
@@ -100,6 +100,66 @@ static bool path_is_absolute(const char *path) {
 #endif
 }
 
+/* Read the "gitdir: <path>" pointer out of a gitlink FILE at <path>/.git.
+ * Returns false when .git is missing, a directory (ordinary repo), or holds no
+ * pointer. A relative pointer is resolved against path. */
+static bool read_gitlink_target(const char *path, char *out, size_t out_size) {
+    char dot_git[GIT_OUTPUT_MAX];
+    int n = snprintf(dot_git, sizeof(dot_git), "%s/.git", path);
+    if (n < 0 || n >= (int)sizeof(dot_git)) {
+        return false;
+    }
+    struct stat st;
+    if (stat(dot_git, &st) != 0 || !S_ISREG(st.st_mode)) {
+        return false;
+    }
+
+    FILE *f = cbm_fopen(dot_git, "r");
+    if (!f) {
+        return false;
+    }
+    char line[GIT_OUTPUT_MAX];
+    bool got = false;
+    while (fgets(line, sizeof(line), f)) {
+        trim_newlines(line);
+        if (strncmp(line, "gitdir:", 7) != 0) {
+            continue;
+        }
+        const char *value = line + 7;
+        while (*value == ' ' || *value == '\t') {
+            value++;
+        }
+        if (!value[0]) {
+            break;
+        }
+        int written = path_is_absolute(value) ? snprintf(out, out_size, "%s", value)
+                                              : snprintf(out, out_size, "%s/%s", path, value);
+        got = written > 0 && written < (int)out_size;
+        break;
+    }
+    fclose(f);
+    return got;
+}
+
+bool cbm_git_is_linked_worktree(const char *path) {
+    if (!path || !path[0]) {
+        return false;
+    }
+    char git_dir[GIT_OUTPUT_MAX];
+    if (!read_gitlink_target(path, git_dir, sizeof(git_dir))) {
+        return false;
+    }
+    /* Only linked worktrees carry <gitdir>/commondir; a submodule gitlink
+     * points at <super>/.git/modules/<name>, which does not. */
+    char commondir[GIT_OUTPUT_MAX];
+    int n = snprintf(commondir, sizeof(commondir), "%s/commondir", git_dir);
+    if (n < 0 || n >= (int)sizeof(commondir)) {
+        return false;
+    }
+    struct stat st;
+    return stat(commondir, &st) == 0 && S_ISREG(st.st_mode);
+}
+
 static char *join_root_relative(const char *root, const char *rel) {
     if (!root || !root[0]) {
         return git_strdup(rel);
 
@@ -19,6 +19,18 @@ typedef struct {
     char *base_sha;
 } cbm_git_context_t;
 
+/* True when path is the root of a LINKED git worktree (`git worktree add`).
+ *
+ * Plumbing-only, no subprocess: <path>/.git must be a regular file holding a
+ * "gitdir: <path>" pointer AND that gitdir must contain a `commondir` file.
+ * The commondir check is what separates a linked worktree from a submodule —
+ * a submodule's .git is also a gitlink file, but its gitdir
+ * (<super>/.git/modules/<name>) has no commondir entry.
+ *
+ * Callers run this on every session start, so it stays fork-free; the richer
+ * cbm_git_context_resolve() shells out to git and is not usable on that path. */
+bool cbm_git_is_linked_worktree(const char *path);
+
 int cbm_git_context_resolve(const char *path, cbm_git_context_t *out);
 void cbm_git_context_free(cbm_git_context_t *ctx);
 char *cbm_git_context_branch_qn(const char *project_name, const cbm_git_context_t *ctx);
 
@@ -478,7 +478,10 @@ static const tool_def_t TOOLS[] = {
      "\"name\":{\"type\":\"string\",\"description\":"
      "\"Name override; Non-ASCII bytes are encoded; unsafe characters normalized.\"},"
      "\"persistence\":{\"type\":\"boolean\",\"default\":false,\"description\":"
-     "\"Write .codebase-memory/graph.db.zst.\"}"
+     "\"Write .codebase-memory/graph.db.zst.\"},"
+     "\"index_worktree\":{\"type\":\"boolean\",\"default\":false,\"description\":"
+     "\"Index repo_path even when it is a linked git worktree and the "
+     "ignore_worktrees config key is enabled. No effect otherwise.\"}"
      "},\"required\":[\"repo_path\"]}"},
 
     {"search_graph",
@@ -11145,6 +11148,20 @@ static char *handle_index_repository(cbm_mcp_server_t *srv, const char *args) {
         return cbm_mcp_text_result(boundary_err, true);
     }
 
+    /* ignore_worktrees: an EXPLICIT index_repository call on a linked worktree
+     * is refused with the two ways forward (per-call override, or turn the
+     * setting off) rather than silently skipped — a silent success would be
+     * indistinguishable from a real index to the caller. */
+    if (cbm_mcp_ignore_worktrees_enabled(srv) && !cbm_mcp_get_bool_arg(args, "index_worktree") &&
+        cbm_git_is_linked_worktree(repo_path)) {
+        index_args_free(repo_path, mode_str, name_override);
+        return cbm_mcp_text_result(
+            "repo_path is a linked git worktree and ignore_worktrees is enabled. Pass "
+            "index_worktree=true to index it anyway, or run: codebase-memory-mcp config set "
+            "ignore_worktrees false",
+            true);
+    }
+
     if (mode_str && strcmp(mode_str, "cross-repo-intelligence") == 0) {
         char *result = handle_cross_repo_mode(srv, repo_path, name_override, args);
         index_args_free(repo_path, mode_str, name_override);
@@ -17569,6 +17586,17 @@ static bool auto_watch_enabled(cbm_mcp_server_t *srv) {
     return cbm_config_get_bool(srv->config, CBM_CONFIG_AUTO_WATCH, true);
 }
 
+/* ignore_worktrees config: gates automatic indexing of LINKED git worktrees
+ * (default off, so existing setups keep indexing them). Users who create many
+ * short-lived worktrees can stop each throwaway checkout from registering a
+ * new permanent project with `config set ignore_worktrees true`. */
+bool cbm_mcp_ignore_worktrees_enabled(const cbm_mcp_server_t *srv) {
+    if (!srv || !srv->config) {
+        return false; /* default off */
+    }
+    return cbm_config_get_bool(srv->config, CBM_CONFIG_IGNORE_WORKTREES, false);
+}
+
 /* Register the session project with the background watcher for ongoing
  * change detection — unless auto_watch is disabled. */
 static void register_watcher_if_enabled(cbm_mcp_server_t *srv) {
@@ -17721,6 +17749,12 @@ static void maybe_auto_index(cbm_mcp_server_t *srv) {
         return;
     }
 
+    if (cbm_mcp_ignore_worktrees_enabled(srv) && cbm_git_is_linked_worktree(srv->session_root)) {
+        cbm_log_info("autoindex.skip", "reason", "linked_worktree", "project",
+                     srv->session_project);
+        return;
+    }
+
     /* Quick tracked-file count check to avoid OOM on massive repos. */
     int file_count = -1;
 #ifdef CBM_ENABLE_TEST_SEAMS
 
@@ -63,6 +63,11 @@ const char *cbm_mcp_edge_strategy_class(const char *strategy);
 bool cbm_mcp_auto_index_within_file_limit(const char *root_path, int file_limit,
                                           int *file_count_out);
 
+/* True when the `ignore_worktrees` config key is on for this server (default
+ * off). Callers pair it with cbm_git_is_linked_worktree() to decide whether an
+ * automatic index of a linked worktree should be skipped. */
+bool cbm_mcp_ignore_worktrees_enabled(const cbm_mcp_server_t *srv);
+
 /* detect_changes seed scoping (#1363): does `node`'s line range overlap any
  * recorded hunk for `file`? Exposed for direct unit testing of the overlap
  * logic, independent of the git/subprocess/index plumbing around it. */