Standardize file I/O to use UTF-8 encoding across all platforms

Replace all slurp/spit calls with UTF-8 utility helpers to ensure
consistent encoding, especially on Windows where JVM defaults to
Windows-1252 instead of UTF-8.

Changes:
- Add clojure-mcp.utils.file namespace with slurp-utf8 and spit-utf8
- Convert all inline slurp/spit :encoding "UTF-8" to use new helpers
- Update 15 source files with file-utils namespace imports
- Add comprehensive tests for new utilities

All 361 tests pass with 2576 assertions.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: Bruce Hauman

src/clojure_mcp/agent/general_agent.clj

@@ -7,7 +7,8 @@
             [clojure-mcp.agent.langchain :as chain]
             [clojure-mcp.config :as config]
             [clojure-mcp.tools.project.core :as project-core]
-            [clojure-mcp.tools :as tools])
+            [clojure-mcp.tools :as tools]
+            [clojure-mcp.utils.file :as file-utils])
   (:import
    [clojure_mcp.agent.langchain AiService]
    [dev.langchain4j.data.message UserMessage TextContent]))
@@ -49,7 +50,7 @@
           context-strings (cond-> []
                             (.exists proj-summary-file)
                             (conj (str "This is a project summary:\n"
-                                       (slurp proj-summary-file)))
+                                       (file-utils/slurp-utf8 proj-summary-file)))
 
                             (and (not error) outputs)
                             (conj (str "This is the current project structure:\n"
@@ -58,7 +59,7 @@
                             (.exists code-index-file)
                             (conj (str "This is a code index of the code in this project.
 Please use it to inform you as to which files should be investigated.\n=======================\n"
-                                       (slurp code-index-file))))]
+                                       (file-utils/slurp-utf8 code-index-file))))]
       context-strings)
 
     (sequential? context-config)
@@ -67,7 +68,7 @@ Please use it to inform you as to which files should be investigated.\n=========
                :when (.exists file)]
            (str "File: " file-path "\n"
                 "=======================\n"
-                (slurp file) "\n\n")))
+                (file-utils/slurp-utf8 file) "\n\n")))
 
     :else
     []))

src/clojure_mcp/code_indexer.clj

@@ -12,6 +12,7 @@
   (:require
    [clojure-mcp.tools.unified-read-file.pattern-core :as pattern]
    [clojure-mcp.tools.glob-files.core :as glob]
+   [clojure-mcp.utils.file :as file-utils]
    [clojure.java.io :as io]
    [clojure.string :as str]))
 
@@ -83,7 +84,7 @@
    Returns a map with :files-indexed, :output-file, and :size-bytes."
   [source-dir output-file]
   (let [indexed-content (index-and-format source-dir)]
-    (spit output-file indexed-content)
+    (file-utils/spit-utf8 output-file indexed-content)
     {:files-indexed (count (find-clojure-files source-dir))
      :output-file output-file
      :size-bytes (count indexed-content)}))
@@ -114,7 +115,7 @@
   [source-dir output-file]
   (let [indexed-files (index-source-directory source-dir)
         indexed-content (format-collapsed-views indexed-files)]
-    (spit output-file indexed-content)
+    (file-utils/spit-utf8 output-file indexed-content)
     {:files-indexed (count indexed-files)
      :output-file output-file
      :size-bytes (count indexed-content)}))
@@ -177,7 +178,7 @@
             (str/join "\n\n" dir-sections))
           (format-collapsed-views all-indexed-files))
 
-        _ (spit out-file formatted-content)
+        _ (file-utils/spit-utf8 out-file formatted-content)
         end-time (System/currentTimeMillis)]
 
     {:files-indexed (count all-indexed-files)

src/clojure_mcp/config.clj

@@ -4,6 +4,7 @@
    [clojure.string :as str]
    [clojure-mcp.dialects :as dialects]
    [clojure-mcp.config.schema :as schema]
+   [clojure-mcp.utils.file :as file-utils]
    [clojure.edn :as edn]
    [clojure.tools.logging :as log]))
 
@@ -23,7 +24,7 @@
   (let [config-file (io/file config-file-path)]
     (if (.exists config-file)
       (try
-        (edn/read-string (slurp config-file))
+        (edn/read-string (file-utils/slurp-utf8 config-file))
         (catch Exception e
           (log/warn e "Failed to read config file:" (.getPath config-file))
           {}))

src/clojure_mcp/dialects.clj

@@ -6,7 +6,8 @@
   (:require [clojure.edn :as edn]
             [clojure.java.io :as io]
             [clojure.tools.logging :as log]
-            [clojure-mcp.nrepl :as nrepl]))
+            [clojure-mcp.nrepl :as nrepl]
+            [clojure-mcp.utils.file :as file-utils]))
 
 (defn handle-bash-over-nrepl? [nrepl-env-type]
   (boolean (#{:clj :bb} nrepl-env-type)))
@@ -65,7 +66,7 @@
 (defmethod load-repl-helpers-exp :clj
   [_]
   ;; For Clojure, we load the helpers from resources
-  [(slurp (io/resource "clojure-mcp/repl_helpers.clj"))
+  [(file-utils/slurp-utf8 (io/resource "clojure-mcp/repl_helpers.clj"))
    "(in-ns 'user)"])
 
 (defmethod load-repl-helpers-exp :default

src/clojure_mcp/prompt_cli.clj

@@ -16,7 +16,8 @@
             [clojure-mcp.agent.general-agent :as general-agent]
             [clojure-mcp.agent.langchain.chat-listener :as listener]
             [clojure-mcp.agent.langchain.message-conv :as msg-conv]
-            [clojure-mcp.tool-format :as tool-format])
+            [clojure-mcp.tool-format :as tool-format]
+            [clojure-mcp.utils.file :as file-utils])
   (:import [dev.langchain4j.data.message ChatMessageSerializer ChatMessageDeserializer]
            [java.time LocalDateTime]
            [java.time.format DateTimeFormatter])
@@ -49,9 +50,7 @@
     (when-not config-source
       (throw (ex-info "Agent configuration not found"
                       {:config-path config-path})))
-    (-> config-source
-        slurp
-        edn/read-string)))
+    (-> config-source file-utils/slurp-utf8 edn/read-string)))
 
 (defn load-system-message
   "Load system message from resource if it's a path, otherwise return as-is"
@@ -60,7 +59,7 @@
            (or (str/ends-with? system-message ".md")
                (str/ends-with? system-message ".txt")))
     (if-let [resource (io/resource system-message)]
-      (slurp resource)
+      (file-utils/slurp-utf8 resource)
       system-message)
     system-message))
 
@@ -95,7 +94,7 @@
                       :created created
                       :messages messages-json}
         json-str (json/write-str session-data :escape-slash false)]
-    (spit session-file json-str)
+    (file-utils/spit-utf8 session-file json-str)
     session-file))
 
 (defn find-latest-session-file
@@ -114,7 +113,7 @@
   "Load a session from a file.
    Returns {:model \"...\" :messages [...]} or throws if file doesn't exist or is invalid."
   [session-file]
-  (let [json-str (slurp session-file)
+  (let [json-str (file-utils/slurp-utf8 session-file)
         session-data (json/read-str json-str :key-fn keyword)
         messages-json (:messages session-data)
         messages (ChatMessageDeserializer/messagesFromJson messages-json)]

src/clojure_mcp/prompts.clj

@@ -5,7 +5,8 @@
             [pogonos.core :as pg]
             [clojure-mcp.config :as config]
             [clojure-mcp.tools.scratch-pad.tool :as scratch-pad]
-            [clojure-mcp.tools.scratch-pad.core :as scratch-pad-core]))
+            [clojure-mcp.tools.scratch-pad.core :as scratch-pad-core]
+            [clojure-mcp.utils.file :as file-utils]))
 
 (defn simple-content-prompt-fn
   "Returns a prompt-fn that ignores request arguments and returns
@@ -20,7 +21,7 @@
   "Loads prompt content from a classpath resource file."
   [filename]
   (if-let [resource (io/resource filename)]
-    (slurp resource)
+    (file-utils/slurp-utf8 resource)
     (str "Error: Prompt file not found on classpath: " filename)))
 
 ;; --- Prompt Definitions ---
@@ -210,7 +211,7 @@ After doing this provide a very brief (8 lines) summary of where we are and then
                   (try
                     ;; Load the file
                     (if (.exists file)
-                      (let [data (clojure.edn/read-string (slurp file))
+                      (let [data (clojure.edn/read-string (file-utils/slurp-utf8 file))
                             ;; Update the scratch pad atom
                             _ (scratch-pad/update-scratch-pad! nrepl-client-atom (constantly data))
                             ;; Get shallow inspect of the data
@@ -262,7 +263,7 @@ After doing this provide a very brief (8 lines) summary of where we are and then
                           (when-not (.exists dir)
                             (.mkdirs dir)))
                         ;; Save the data
-                        (spit file (pr-str current-data))
+                        (file-utils/spit-utf8 file (pr-str current-data))
                         ;; Get shallow inspect for confirmation
                         (let [inspect-result (:result (scratch-pad-core/execute-inspect current-data 1 nil))]
                           (clj-result-k
@@ -323,7 +324,7 @@ and using the following format:
                                                        file-path
                                                        (.getCanonicalPath (io/file working-dir file-path)))]
                                        (when (.exists (io/file full-path))
-                                         (slurp full-path)))
+                                         (file-utils/slurp-utf8 full-path)))
                            :else nil)]
     (when template-content
       {:name prompt-name

src/clojure_mcp/resources.clj

@@ -6,14 +6,15 @@
             [clojure-mcp.nrepl :as mcp-nrepl]
             [clojure-mcp.config :as config]
             [clojure-mcp.file-content :as file-content]
-            [clojure-mcp.tools.project.core :as project])
+            [clojure-mcp.tools.project.core :as project]
+            [clojure-mcp.utils.file :as file-utils])
   (:import [io.modelcontextprotocol.spec McpSchema$Resource McpSchema$ReadResourceResult]))
 
 (defn read-file [full-path]
   (let [file (io/file full-path)]
     (if (.exists file)
       (try
-        (slurp file)
+        (file-utils/slurp-utf8 file)
         (catch Exception e
           (throw (ex-info (str "reading file- " full-path
                                "\nException- " (.getMessage e))

src/clojure_mcp/tools/agent_tool_builder/file_changes.clj

@@ -3,6 +3,7 @@
   (:require
    [clojure.java.io :as io]
    [clojure-mcp.utils.diff :as diff-utils]
+   [clojure-mcp.utils.file :as file-utils]
    [clojure.string :as str]
    [clojure.tools.logging :as log]))
 
@@ -86,7 +87,7 @@
         (let [diffs (for [[canonical-path original-content] changed-files]
                       (let [current-file (io/file canonical-path)]
                         (if (.exists current-file)
-                          (let [current-content (slurp current-file)]
+                          (let [current-content (file-utils/slurp-utf8 current-file)]
                             (format-file-diff canonical-path original-content current-content))
                           ;; File was deleted
                           (format-file-diff canonical-path original-content ""))))]

src/clojure_mcp/tools/file_edit/core.clj

@@ -3,7 +3,8 @@
    This namespace contains the pure functionality without any MCP-specific code."
   (:require
    [clojure.java.io :as io]
-   [clojure.string :as str]))
+   [clojure.string :as str]
+   [clojure-mcp.utils.file :as file-utils]))
 
 (defn load-file-content
   "Load file content from a path.
@@ -19,7 +20,7 @@
   (try
     (let [file (io/file path)]
       (if (.exists file)
-        {:content (slurp file)
+        {:content (file-utils/slurp-utf8 file)
          :error false}
         {:error true
          :message (str "File not found: " path)}))
@@ -130,7 +131,7 @@
       ;; Create parent directories if they don't exist
       (when (and parent (not (.exists parent)))
         (.mkdirs parent))
-      (spit file content)
+      (file-utils/spit-utf8 file content)
       {:success true})
     (catch Exception e
       {:success false

src/clojure_mcp/tools/file_write/core.clj

@@ -7,7 +7,8 @@
    [clojure-mcp.utils.diff :as diff-utils]
    [clojure-mcp.linting :as linting]
    [clojure-mcp.utils.valid-paths :as valid-paths]
-   [rewrite-clj.zip :as z]))
+   [rewrite-clj.zip :as z]
+   [clojure-mcp.utils.file :as file-utils]))
 
 (defn is-clojure-file?
   "Check if a file is a Clojure-related file based on its extension or Babashka shebang.
@@ -32,7 +33,7 @@
   [nrepl-client-atom file-path content dry_run]
   (let [file (io/file file-path)
         file-exists? (.exists file)
-        old-content (if file-exists? (slurp file) "")
+        old-content (if file-exists? (file-utils/slurp-utf8 file) "")
 
         ;; Create a context map for the pipeline
         initial-ctx {::pipeline/nrepl-client-atom nrepl-client-atom
@@ -95,7 +96,7 @@
   (try
     (let [file (io/file file-path)
           file-exists? (.exists file)
-          old-content (if file-exists? (slurp file) "")
+          old-content (if file-exists? (file-utils/slurp-utf8 file) "")
           ;; Only generate diff if the file already exists
           diff (if file-exists?
                  (if (= old-content content)
@@ -119,7 +120,7 @@
         ;; Normal operation - write and return full result
         :else
         (do
-          (spit file content)
+          (file-utils/spit-utf8 file content)
           {:error false
            :type (if file-exists? "update" "create")
            :file-path file-path