Migrate from clojure.tools.logging to Timbre (#131)

* Migrate from clojure.tools.logging to Timbre

Replace clojure.tools.logging with taoensso.timbre for pure Clojure logging.

Changes:
- Create src/clojure_mcp/logging.clj with centralized Timbre configuration
- Add logging initialization to all main entry points (main.clj, sse_main.clj,
  figwheel_main.clj, shadow_main.clj)
- Update all 26 source files to use [taoensso.timbre :as log]
- Add test/clojure_mcp/test_helper.clj to suppress logging during tests
- Update :test alias in deps.edn to use -M flag with test helper
- Add helpful error message when using -X:test instead of -M:test
- Remove clojure.tools.logging and logback dependencies
- Add slf4j-nop to main deps to suppress Java library logging
- Delete dev/logback.xml (no longer needed)

Benefits:
- Pure Clojure logging solution (no Java dependencies)
- Simplified configuration
- Better REPL integration
- Clean test output with zero logging noise
- Consistent logging across all entry points

* chagne logging defaults

---------

Co-authored-by: Bruce Hauman <bhauman@gmail.com>

Author: bhauman

deps.edn

@@ -2,7 +2,6 @@
  :deps {org.clojure/clojure {:mvn/version "1.12.1"}
         org.clojure/data.json {:mvn/version "2.5.1"}
         nrepl/nrepl {:mvn/version "1.3.1"}
-        org.clojure/tools.logging {:mvn/version "1.3.0"}
         org.clojure/tools.cli {:mvn/version "1.1.230"}
         org.clj-commons/pretty {:mvn/version "3.6.7"}
 
@@ -27,22 +26,22 @@
         dev.langchain4j/langchain4j-anthropic {:mvn/version "1.8.0"}
         dev.langchain4j/langchain4j-google-ai-gemini {:mvn/version "1.8.0"}
 
-        ;; in order to use the stdio server you have to handle logging somehow
-        ;; org.slf4j/slf4j-nop {:mvn/version "2.0.16"}
+        com.taoensso/timbre {:mvn/version "6.8.0"}
+
+        ;; Suppress logging from Java libraries (MCP SDK, LangChain4j, etc.)
+        org.slf4j/slf4j-nop {:mvn/version "2.0.16"}
 
         ;; native Java diff library
         io.github.java-diff-utils/java-diff-utils {:mvn/version "4.15"}}
  :aliases
 
  {:mcp
-  {:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
-   :exec-fn clojure-mcp.main/start-mcp-server
+  {:exec-fn clojure-mcp.main/start-mcp-server
    ;; it needs an nrepl port to talk to
    :exec-args {:port 7888}}
 
   :mcp-sse
-  {:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"} ;; optional 
-                jakarta.servlet/jakarta.servlet-api {:mvn/version "6.1.0"}
+  {:extra-deps {jakarta.servlet/jakarta.servlet-api {:mvn/version "6.1.0"}
                 org.eclipse.jetty/jetty-server {:mvn/version "11.0.20"}
                 org.eclipse.jetty/jetty-servlet {:mvn/version "11.0.20"}}
    :exec-fn clojure-mcp.sse-main/start-sse-mcp-server
@@ -52,86 +51,72 @@
                :mcp-sse-port 8078}}
 
   :mcp-figwheel
-  {:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
-   :exec-fn clojure-mcp.main-examples.figwheel-main/start-mcp-server
+  {:exec-fn clojure-mcp.main-examples.figwheel-main/start-mcp-server
    :exec-args {:port 7888 :figwheel-build "dev"}}
 
   :mcp-shadow
-  {:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
-   :exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
+  {:exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
    :exec-args {:port 7888 :shadow-build "app"}}
 
   ;; dual shadow and project nrepl setup
   :mcp-shadow-dual
-  {:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
-   :extra-paths ["dev" "test"]
+  {:extra-paths ["dev" "test"]
    :exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
    ;; it needs an nrepl port to talk to
    :exec-args {:port 7888 :shadow-build "app" :shadow-port 7889}}
 
-  ;; below are dev set ups that need a logback.xml file
+  ;; below are dev set ups
   :prompt-cli
-  {:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
-   :main-opts ["-m" "clojure-mcp.prompt-cli"]}
+  {:main-opts ["-m" "clojure-mcp.prompt-cli"]}
 
   :dev-mcp
-  {:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
-   :extra-paths ["dev" "test"]
+  {:extra-paths ["dev" "test"]
    :exec-fn clojure-mcp.main/start-mcp-server
    ;; it needs an nrepl port to talk to
    :exec-args {:port 7888
                ;; test auto starting the repl
                ;; :start-nrepl-cmd ["clojure" "-M:nrepl"]
                }}
 
-  ;; DEV setup needs logback.xml
   :dev-mcp-figwheel
-  {:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
-   :extra-paths ["dev" "test"]
+  {:extra-paths ["dev" "test"]
    :exec-fn clojure-mcp.main-examples.figwheel-main/start-mcp-server
    ;; it needs an nrepl port to talk to
    :exec-args {:port 7888 :figwheel-build "dev"}}
 
-  ;; DEV setup needs logback.xml
   :dev-mcp-shadow
-  {:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
-   :extra-paths ["dev" "test"]
+  {:extra-paths ["dev" "test"]
    :exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
    ;; it needs an nrepl port to talk to
    :exec-args {:port 7888 :shadow-build "app"}}
 
   :dev-mcp-shadow-dual
-  {:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
-   :extra-paths ["dev" "test"]
+  {:extra-paths ["dev" "test"]
    :exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
    ;; it needs an nrepl port to talk to
    :exec-args {:port 7888 :shadow-build "app" :shadow-port 7889}}
 
   :nrepl {:extra-paths ["test" "dev"]
-          :extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
           :main-opts ["-m" "nrepl.cmdline" "--port" "7888"]}
 
   :dkr-nrepl {:extra-paths ["test" "dev"]
-              :extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
               :main-opts ["-m" "nrepl.cmdline" "--port" "7888"
                           ;; for Docker
                           "--bind" "0.0.0.0"]}
 
   ;; dev cycle
   :test
   {:extra-paths ["test" "dev"]
-   :exec-fn cognitect.test-runner/test
-   :extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}
-                org.clojure/test.check {:mvn/version "1.1.1"}
+   :exec-fn clojure-mcp.test-helper/run-tests-with-exec
+   :extra-deps {org.clojure/test.check {:mvn/version "1.1.1"}
                 nrepl/nrepl {:mvn/version "1.3.1"} ;; Add nrepl server for testing
                 io.github.cognitect-labs/test-runner
                 {:git/tag "v0.5.1" :git/sha "dfb30dd"}}
-   :main-opts ["-m" "cognitect.test-runner"]}
+   :main-opts ["-e" "(require 'clojure-mcp.test-helper)" "-m" "cognitect.test-runner"]}
 
   :index
   {:exec-fn clojure-mcp.code-indexer/map-project
    :exec-args {}
-   :extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
    ;; Override with: clojure -X:index :dirs '["src" "lib"]' :include-tests true :out-file '"my-index.txt"'
    }
 

dev/logback.xml

@@ -2,7 +2,7 @@
   "A generalized agent library that can be parameterized with system prompts,
    context, tools, memory, and models."
   (:require [clojure.string :as string]
-            [clojure.tools.logging :as log]
+            [taoensso.timbre :as log]
             [clojure.java.io :as io]
             [clojure-mcp.agent.langchain :as chain]
             [clojure-mcp.tools.project.core :as project-core]

src/clojure_mcp/agent/general_agent.clj

@@ -2,7 +2,7 @@
   (:require
    [clojure.data.json :as json]
    [clojure-mcp.agent.langchain.schema :as schema]
-   [clojure.tools.logging :as log]
+   [taoensso.timbre :as log]
    [clojure.string :as string]
    [clojure.pprint])
   (:import

src/clojure_mcp/agent/langchain.clj

@@ -2,7 +2,7 @@
   "Creates ChatModelListener instances from Clojure functions that work with EDN data"
   (:require
    [clojure-mcp.agent.langchain.message-conv :as msg-conv]
-   [clojure.tools.logging :as log])
+   [taoensso.timbre :as log])
   (:import
    [dev.langchain4j.model.chat.listener
     ChatModelListener

src/clojure_mcp/agent/langchain/chat_listener.clj

@@ -2,7 +2,7 @@
   (:require
    [clojure-mcp.config.schema :as schema]
    [clojure-mcp.config :as config]
-   [clojure.tools.logging :as log])
+   [taoensso.timbre :as log])
   (:import
    [dev.langchain4j.model.anthropic
     AnthropicChatModel

src/clojure_mcp/agent/langchain/model.clj

@@ -4,7 +4,7 @@
    [clojure-mcp.config.schema :as schema]
    [clojure-mcp.utils.file :as file-utils]
    [clojure.edn :as edn]
-   [clojure.tools.logging :as log]))
+   [taoensso.timbre :as log]))
 
 (defn- relative-to [dir path]
   (try

src/clojure_mcp/config.clj

@@ -2,7 +2,7 @@
   (:require [clojure.data.json :as json]
             [clojure.java.io :as io]
             [clojure.spec.alpha :as s]
-            [clojure.tools.logging :as log]
+            [taoensso.timbre :as log]
             [clojure-mcp.nrepl :as nrepl]
             [clojure-mcp.config :as config]
             [clojure-mcp.dialects :as dialects]

src/clojure_mcp/core.clj

@@ -5,7 +5,7 @@
    and initialization sequences specific to each dialect."
   (:require [clojure.edn :as edn]
             [clojure.java.io :as io]
-            [clojure.tools.logging :as log]
+            [taoensso.timbre :as log]
             [clojure-mcp.nrepl :as nrepl]
             [clojure-mcp.utils.file :as file-utils]))
 

src/clojure_mcp/dialects.clj

@@ -0,0 +1,71 @@
+(ns clojure-mcp.logging
+  "Centralized logging configuration using Timbre.
+
+   This namespace provides functions to configure Timbre-based logging
+   for the Clojure MCP server with support for both development and
+   production modes."
+  (:require [taoensso.timbre :as timbre]))
+
+(def default-log-file ".clojure-mcp/clojure-mcp.log")
+
+(defn configure-logging!
+  "Configure Timbre logging with the given options.
+
+   Options:
+   - :log-file       Path to log file (default: 'logs/clojure-mcp.log')
+   - :enable-logging? Whether to enable logging (default: true)
+   - :log-level      Minimum log level (default: :debug)
+                     Valid values: :trace :debug :info :warn :error :fatal :report
+
+   Examples:
+
+   Development mode with full logging:
+   (configure-logging! {:log-file \"logs/clojure-mcp.log\"
+                        :enable-logging? true
+                        :log-level :debug})
+
+   Production mode with logging suppressed:
+   (configure-logging! {:enable-logging? false})"
+  [{:keys [log-file enable-logging? log-level]
+    :or {log-file default-log-file
+         enable-logging? false
+         log-level :debug}}]
+  (timbre/set-config!
+   {:appenders (if enable-logging?
+                 {:spit (assoc
+                         (timbre/spit-appender {:fname log-file})
+                         :enabled? enable-logging?
+                         :min-level (or log-level :report)
+                         :ns-filter (if enable-logging?
+                                      {:allow #{"clojure-mcp.*"}}
+                                      {:deny #{"*"}}))}
+                 {})}))
+
+(defn configure-dev-logging!
+  "Configure logging for development mode with debug level.
+   Convenience function that enables full debug logging to logs/clojure-mcp.log"
+  []
+  (configure-logging! {:log-file "logs/clojure-mcp.log"
+                       :enable-logging? true
+                       :log-level :debug}))
+
+(defn configure-prod-logging!
+  "Configure logging for production mode with all logging suppressed.
+   Convenience function that disables all logging."
+  []
+  (configure-logging! {:enable-logging? false}))
+
+(defn configure-test-logging!
+  "Configure logging for test mode with all logging suppressed.
+   Convenience function that disables all logging during tests."
+  []
+  (configure-logging! {:enable-logging? false}))
+
+(defn suppress-logging-for-tests!
+  "Automatically suppress logging if running in test mode.
+   Checks for CLOJURE_MCP_TEST environment variable or
+   clojure.mcp.test system property."
+  []
+  (when (or (System/getenv "CLOJURE_MCP_TEST")
+            (System/getProperty "clojure.mcp.test"))
+    (configure-test-logging!)))