Fix clj-kondo warnings: replace :refer :all, remove redundant let, fix docstring placement

- Replace :refer :all with explicit :refer [deftest is testing] in 23 test files
- Remove 17 redundant let expressions across test files
- Fix 10 misplaced docstrings to follow proper Clojure style

All tests pass (295 tests, 2085 assertions, 0 failures)

Author: Bruce Hauman

src/clojure_mcp/agent/langchain/model.clj

@@ -498,7 +498,7 @@
    (create-model-builder-from-config nrepl-client-map model-key {} {}))
   ([nrepl-client-map model-key config-overrides]
    (create-model-builder-from-config nrepl-client-map model-key config-overrides {:validate? true}))
-  ([nrepl-client-map model-key config-overrides {:keys [validate?] :or {validate? true} :as options}]
+  ([nrepl-client-map model-key config-overrides {:keys [validate?] :or {validate? true} :as _options}]
    (let [user-models (config/get-models nrepl-client-map)
          ;; Look in user config first, then defaults
          base-config (or (get user-models model-key)

src/clojure_mcp/agent/langchain/schema.clj

@@ -86,7 +86,7 @@
       (.items (edn->sch items))
       (.build)))
 
-(defmethod edn->sch :object [{:keys [properties description required] :as object}]
+(defmethod edn->sch :object [{:keys [properties description required] :as _object}]
   (let [obj-build
         (cond-> (JsonObjectSchema/builder)
           (not (string/blank? description)) (.description description)

src/clojure_mcp/core.clj

@@ -457,7 +457,7 @@
   [nrepl-client-atom working-dir {:keys [make-tools-fn
                                          make-prompts-fn
                                          make-resources-fn]
-                                  :as component-factories}]
+                                  :as _component-factories}]
   {:tools (when make-tools-fn
             (doall (make-tools-fn nrepl-client-atom working-dir)))
    :prompts (when make-prompts-fn

src/clojure_mcp/file_content.clj

@@ -79,7 +79,7 @@
     (McpSchema$EmbeddedResource. nil nil blob)))
 
 (defn file-response->file-content [{:keys [::file-response]}]
-  (let [{:keys [nio-path mime-type] :as ser-file} (serialized-file file-response)]
+  (let [{:keys [mime-type] :as ser-file} (serialized-file file-response)]
     (cond
       (text-media-type? mime-type) (text-resource-content ser-file)
       (image-media-type? mime-type) (image-content ser-file)

src/clojure_mcp/main.clj

@@ -6,15 +6,15 @@
 
 ;; Delegate to resources namespace
 ;; Note: working-dir param kept for compatibility with core API but unused
-(defn make-resources [nrepl-client-atom working-dir]
+(defn make-resources [nrepl-client-atom _working-dir]
   (resources/make-resources nrepl-client-atom))
 
 ;; Delegate to prompts namespace
 ;; Note: working-dir param kept for compatibility with core API but unused
-(defn make-prompts [nrepl-client-atom working-dir]
+(defn make-prompts [nrepl-client-atom _working-dir]
   (prompts/make-prompts nrepl-client-atom))
 
-(defn make-tools [nrepl-client-atom working-directory]
+(defn make-tools [nrepl-client-atom _working-directory]
   ;; Use the refactored tools builder
   ;; Note: working-directory param kept for compatibility with core API but unused
   (tools/build-all-tools nrepl-client-atom))
@@ -26,7 +26,7 @@
   ([working-dir nrepl-client-atom]
    (make-prompts nrepl-client-atom working-dir)))
 
-(defn ^:deprecated my-resources [nrepl-client-atom working-dir]
+(defn ^:deprecated my-resources [nrepl-client-atom _working-dir]
   (resources/make-resources nrepl-client-atom))
 
 (defn ^:deprecated my-tools [nrepl-client-atom]

src/clojure_mcp/main_examples/shadow_main.clj

@@ -50,7 +50,7 @@ JavaScript interop is fully supported including `js/console.log`, `js/setTimeout
     cljs-session))
 
 ;; when having a completely different connection for cljs
-(defn shadow-eval-tool-secondary-connection-tool [nrepl-client-atom {:keys [shadow-port shadow-build shadow-watch] :as config}]
+(defn shadow-eval-tool-secondary-connection-tool [nrepl-client-atom {:keys [shadow-port _shadow-build _shadow-watch] :as config}]
   (let [cljs-nrepl-client-map (core/create-additional-connection nrepl-client-atom {:port shadow-port})
         cljs-nrepl-client-atom (atom cljs-nrepl-client-map)]
     (start-shadow-repl
@@ -62,7 +62,7 @@ JavaScript interop is fully supported including `js/console.log`, `js/setTimeout
         (assoc :description description))))
 
 ;; when sharing the clojure and cljs repl
-(defn shadow-eval-tool [nrepl-client-atom {:keys [shadow-build shadow-watch] :as config}]
+(defn shadow-eval-tool [nrepl-client-atom {:keys [_shadow-build _shadow-watch] :as config}]
   (let [cljs-session (nrepl/new-session @nrepl-client-atom)
         _ (start-shadow-repl nrepl-client-atom cljs-session config)]
     (-> (eval-tool/eval-code nrepl-client-atom {:nrepl-session cljs-session})
@@ -74,7 +74,7 @@ JavaScript interop is fully supported including `js/console.log`, `js/setTimeout
 ;; 2. or the user starts two processes one for clojure and then we connect to shadow
 ;;    as a secondary connection
 
-(defn make-tools [nrepl-client-atom working-directory & [{:keys [port shadow-port shadow-build shadow-watch] :as config}]]
+(defn make-tools [nrepl-client-atom working-directory & [{:keys [port shadow-port _shadow-build _shadow-watch] :as config}]]
   (if (and port shadow-port (not= port shadow-port))
     (conj (main/make-tools nrepl-client-atom working-directory)
           (shadow-eval-tool-secondary-connection-tool nrepl-client-atom config))

src/clojure_mcp/prompt_cli.clj

@@ -395,7 +395,7 @@
 (defn -main
   "Main entry point for the CLI"
   [& args]
-  (let [{:keys [options arguments errors summary]}
+  (let [{:keys [options _arguments errors summary]}
         (cli/parse-opts args cli-options)]
 
     (cond

src/clojure_mcp/prompts.clj

@@ -243,7 +243,7 @@ After doing this provide a very brief (8 lines) summary of where we are and then
 (def save-new-prompt
   {:name "save_new_prompt"
    :description "Asks the user for a new prompt and a name, and saves them to their user config"
-   :prompt-fn (fn [_ request-args clj-result-k]
+   :prompt-fn (fn [_ _request-args clj-result-k]
                 (clj-result-k
                  {:description "Help user create/update a custom prompt"
                   :messages [{:role :user
@@ -269,7 +269,7 @@ and using the following format:
   "Creates a prompt from configuration map.
    Config should have :description, :args, and either :file-path or :content.
    Uses pogonos/mustache templating for the content."
-  [prompt-name {:keys [description args file-path content]} working-dir nrepl-client-atom]
+  [prompt-name {:keys [description args file-path content]} working-dir _nrepl-client-atom]
   (let [;; Prepare arguments structure for MCP
         arguments (mapv (fn [{:keys [name description required?]}]
                           {:name name

src/clojure_mcp/resources.clj

@@ -43,7 +43,7 @@
    Accepts nrepl-client-atom for consistency with create-file-resource, but doesn't use it.
 
    :contents should be a vector of strings"
-  [url name description mime-type contents & [nrepl-client-atom]]
+  [url name description mime-type contents & [_nrepl-client-atom]]
   {:url url
    :name name
    :description description

src/clojure_mcp/sexp/match.clj

@@ -66,7 +66,7 @@
   (loop [loc zloc]
     (when-not (z/end? loc)
       (let [form (try (z/sexpr loc)
-                      (catch Exception e
+                      (catch Exception _e
                         ::continue))]
         (if (= ::continue form)
           (recur (z/next loc))