diff --git a/.gitignore b/.gitignore
old mode 100644
new mode 100755
diff --git a/Dockerfile b/Dockerfile
old mode 100644
new mode 100755
diff --git a/Makefile b/Makefile
old mode 100644
new mode 100755
diff --git a/README.md b/README.md
old mode 100644
new mode 100755
diff --git a/auth.h b/auth.h
old mode 100644
new mode 100755
diff --git a/browse.c b/browse.c
old mode 100644
new mode 100755
diff --git a/browse.h b/browse.h
old mode 100644
new mode 100755
diff --git a/chat.h b/chat.h
index 11d42ee..8e2a2a8 100644
--- a/chat.h
+++ b/chat.h
@@ -51,8 +51,8 @@ char *chat_json(const char *role, const char *message) {
 
   if (role != NULL && message != NULL) {
     message_add(role, message);
-    if(use_tools()){
-        json_object_object_add(root_object, "tools", tools_descriptions());
+    if (use_tools()) {
+      json_object_object_add(root_object, "tools", tools_descriptions());
     }
   }
 
diff --git a/cmd.sh b/cmd.sh
old mode 100644
new mode 100755
diff --git a/compose.yml b/compose.yml
old mode 100644
new mode 100755
diff --git a/database.db b/database.db
old mode 100644
new mode 100755
diff --git a/db_utils.c b/db_utils.c
old mode 100644
new mode 100755
diff --git a/db_utils.h b/db_utils.h
old mode 100644
new mode 100755
diff --git a/http_curl.h b/http_curl.h
index 95862c9..8111fa8 100644
--- a/http_curl.h
+++ b/http_curl.h
@@ -68,7 +68,8 @@ char *curl_post(const char *url, const char *data) {
     curl_easy_setopt(curl, CURLOPT_URL, url);
     headers = curl_slist_append(headers, "Content-Type: application/json");
     char bearer_header[1337];
-    snprintf(bearer_header, sizeof(bearer_header), "Authorization: Bearer %s", resolve_api_key());
+    snprintf(bearer_header, sizeof(bearer_header), "Authorization: Bearer %s",
+             resolve_api_key());
     headers = curl_slist_append(headers, bearer_header);
     curl_easy_setopt(curl, CURLOPT_HTTPHEADER, headers);
     curl_easy_setopt(curl, CURLOPT_POSTFIELDS, data);
@@ -102,7 +103,8 @@ char *curl_get(const char *url) {
     curl_easy_setopt(curl, CURLOPT_URL, url);
     headers = curl_slist_append(headers, "Content-Type: application/json");
     char bearer_header[1337];
-    snprintf(bearer_header, sizeof(bearer_header), "Authorization: Bearer %s", resolve_api_key());
+    snprintf(bearer_header, sizeof(bearer_header), "Authorization: Bearer %s",
+             resolve_api_key());
     headers = curl_slist_append(headers, bearer_header);
     curl_easy_setopt(curl, CURLOPT_HTTPHEADER, headers);
     curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, WriteCallback);
diff --git a/indexer.h b/indexer.h
old mode 100644
new mode 100755
diff --git a/line.h b/line.h
old mode 100644
new mode 100755
diff --git a/main.c b/main.c
index cdc62cb..942c705 100644
--- a/main.c
+++ b/main.c
@@ -1,8 +1,8 @@
-#include "r.h"
 #include "db_utils.h"
 #include "line.h"
 #include "markdown.h"
 #include "openai.h"
+#include "r.h"
 #include "tools.h"
 #include "utils.h"
 
@@ -12,8 +12,8 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <unistd.h>
 #include <time.h>
+#include <unistd.h>
 
 volatile sig_atomic_t sigint_count = 0;
 time_t first_sigint_time = 0;
@@ -29,259 +29,263 @@ static void repl(void);
 static void init(void);
 static void handle_sigint(int sig);
 
-char * get_env_string(){
-    FILE *fp = popen("env", "r");
-    if (fp == NULL) {
-        perror("popen failed");
-        return NULL;
-    }
+char *get_env_string() {
+  FILE *fp = popen("env", "r");
+  if (fp == NULL) {
+    perror("popen failed");
+    return NULL;
+  }
 
-    size_t buffer_size = 1024;
-    size_t total_size = 0;
-    char *output = malloc(buffer_size);
-    if (output == NULL) {
-        perror("malloc failed");
+  size_t buffer_size = 1024;
+  size_t total_size = 0;
+  char *output = malloc(buffer_size);
+  if (output == NULL) {
+    perror("malloc failed");
+    pclose(fp);
+    return NULL;
+  }
+
+  size_t bytes_read;
+  while ((bytes_read = fread(output + total_size, 1, buffer_size - total_size,
+                             fp)) > 0) {
+    total_size += bytes_read;
+    if (total_size >= buffer_size) {
+      buffer_size *= 2;
+      char *temp = realloc(output, buffer_size);
+      if (temp == NULL) {
+        perror("realloc failed");
+        free(output);
         pclose(fp);
         return NULL;
+      }
+      output = temp;
     }
+  }
 
-    size_t bytes_read;
-    while ((bytes_read = fread(output + total_size, 1, buffer_size - total_size, fp)) > 0) {
-        total_size += bytes_read;
-        if (total_size >= buffer_size) {
-            buffer_size *= 2;
-            char *temp = realloc(output, buffer_size);
-            if (temp == NULL) {
-                perror("realloc failed");
-                free(output);
-                pclose(fp);
-                return NULL;
-            }
-            output = temp;
-        }
-    }
+  // Null-terminate the output
+  output[total_size] = '\0';
 
-    // Null-terminate the output
-    output[total_size] = '\0';
-
-
-    pclose(fp);
-    return output;
+  pclose(fp);
+  return output;
 }
 
 static char *get_prompt_from_stdin(char *prompt) {
-    int index = 0;
-    int c;
-    while ((c = getchar()) != EOF) {
-        prompt[index++] = (char)c;
-    }
-    prompt[index] = '\0';
-    return prompt;
+  int index = 0;
+  int c;
+  while ((c = getchar()) != EOF) {
+    prompt[index++] = (char)c;
+  }
+  prompt[index] = '\0';
+  return prompt;
 }
 
 static char *get_prompt_from_args(int argc, char **argv) {
-    char *prompt = malloc(10 * 1024 * 1024 + 1);
-    char *system = malloc(1024 * 1024);
-    if (!prompt || !system) {
-        fprintf(stderr, "Error: Memory allocation failed.\n");
-        free(prompt);
-        free(system);
-        return NULL;
-    }
+  char *prompt = malloc(10 * 1024 * 1024 + 1);
+  char *system = malloc(1024 * 1024);
+  if (!prompt || !system) {
+    fprintf(stderr, "Error: Memory allocation failed.\n");
+    free(prompt);
+    free(system);
+    return NULL;
+  }
 
-    bool get_from_std_in = false;
+  bool get_from_std_in = false;
 
-    for (int i = 1; i < argc; i++) {
-        if (strcmp(argv[i], "--stdin") == 0) {
-            fprintf(stderr, "Reading from stdin.\n");
-            get_from_std_in = true;
-        } else if (strcmp(argv[i], "--verbose") == 0) {
-            is_verbose = true;
-        } else if (strcmp(argv[i], "--py") == 0 && i + 1 < argc) {
-            char *py_file_path = expand_home_directory(argv[++i]);
-            fprintf(stderr, "Including \"%s\".\n", py_file_path);
-            openai_include(py_file_path);
-            free(py_file_path);
-        } else if (strcmp(argv[i], "--free") == 0) {
-            auth_free();
-        } else if (strcmp(argv[i], "--context") == 0 && i + 1 < argc) {
-            char *context_file_path = argv[++i];
-            fprintf(stderr, "Including \"%s\".\n", context_file_path);
-            openai_include(context_file_path);
-        } else if (strcmp(argv[i], "--api") == 0) {
-            API_MODE = true;
-        } else if (strcmp(argv[i], "--nh") == 0) {
-            SYNTAX_HIGHLIGHT_ENABLED = false;
-            fprintf(stderr, "Syntax highlighting disabled.\n");
-        } else {
-            strcat(system, argv[i]);
-            strcat(system, (i < argc - 1) ? " " : ".");
-        }
-    }
-
-    if (get_from_std_in) {
-        if (*system)
-            openai_system(system);
-        prompt = get_prompt_from_stdin(prompt);
+  for (int i = 1; i < argc; i++) {
+    if (strcmp(argv[i], "--stdin") == 0) {
+      fprintf(stderr, "Reading from stdin.\n");
+      get_from_std_in = true;
+    } else if (strcmp(argv[i], "--verbose") == 0) {
+      is_verbose = true;
+    } else if (strcmp(argv[i], "--py") == 0 && i + 1 < argc) {
+      char *py_file_path = expand_home_directory(argv[++i]);
+      fprintf(stderr, "Including \"%s\".\n", py_file_path);
+      openai_include(py_file_path);
+      free(py_file_path);
+    } else if (strcmp(argv[i], "--free") == 0) {
+      auth_free();
+    } else if (strcmp(argv[i], "--context") == 0 && i + 1 < argc) {
+      char *context_file_path = argv[++i];
+      fprintf(stderr, "Including \"%s\".\n", context_file_path);
+      openai_include(context_file_path);
+    } else if (strcmp(argv[i], "--api") == 0) {
+      API_MODE = true;
+    } else if (strcmp(argv[i], "--nh") == 0) {
+      SYNTAX_HIGHLIGHT_ENABLED = false;
+      fprintf(stderr, "Syntax highlighting disabled.\n");
     } else {
-        free(prompt);
-        prompt = system;
+      strcat(system, argv[i]);
+      strcat(system, (i < argc - 1) ? " " : ".");
     }
+  }
 
-    if (!*prompt) {
-        free(prompt);
-        return NULL;
-    }
-    return prompt;
+  if (get_from_std_in) {
+    if (*system)
+      openai_system(system);
+    prompt = get_prompt_from_stdin(prompt);
+  } else {
+    free(prompt);
+    prompt = system;
+  }
+
+  if (!*prompt) {
+    free(prompt);
+    return NULL;
+  }
+  return prompt;
 }
 
 static bool try_prompt(int argc, char *argv[]) {
-    char *prompt = get_prompt_from_args(argc, argv);
-    if (prompt) {
-        char *response = openai_chat("user", prompt);
-        if (!response) {
-            printf("Could not get response from server\n");
-            free(prompt);
-            return false;
-        }
-        render(response);
-        free(response);
-        free(prompt);
-        return true;
+  char *prompt = get_prompt_from_args(argc, argv);
+  if (prompt) {
+    char *response = openai_chat("user", prompt);
+    if (!response) {
+      printf("Could not get response from server\n");
+      free(prompt);
+      return false;
     }
-    return false;
+    render(response);
+    free(response);
+    free(prompt);
+    return true;
+  }
+  return false;
 }
 
 static bool openai_include(const char *path) {
-    char *file_content = read_file(path);
-    if (!file_content)
-        return false;
+  char *file_content = read_file(path);
+  if (!file_content)
+    return false;
 
-    openai_system(file_content);
-    free(file_content);
-    return true;
+  openai_system(file_content);
+  free(file_content);
+  return true;
 }
 
 static void render(const char *content) {
-    if (SYNTAX_HIGHLIGHT_ENABLED) {
-        parse_markdown_to_ansi(content);
-    } else {
-        printf("%s", content);
-    }
+  if (SYNTAX_HIGHLIGHT_ENABLED) {
+    parse_markdown_to_ansi(content);
+  } else {
+    printf("%s", content);
+  }
 }
 
 static void repl(void) {
-    line_init();
-    char *line = NULL;
+  line_init();
+  char *line = NULL;
 
-    while (true) {
-        line = line_read("> ");
-        if (!line || !*line)
-            continue;
+  while (true) {
+    line = line_read("> ");
+    if (!line || !*line)
+      continue;
 
-        if (!strncmp(line, "!dump", 5)) {
-            printf("%s\n", message_json());
-            continue;
-        }
-        if (!strncmp(line, "!verbose", 8)) {
-            is_verbose = !is_verbose;
-            fprintf(stderr, "%s\n", is_verbose ? "Verbose mode enabled" : "Verbose mode disabled");
-            continue;
-        }
-        if (line && *line != '\n')
-            line_add_history(line);
-        if (!strncmp(line, "!tools", 6)) {
-            printf("Available tools: %s\n", json_object_to_json_string(tools_descriptions()));
-            continue;
-        }
-        if (!strncmp(line, "!models", 7)) {
-            printf("Current model: %s\n", openai_fetch_models());
-            continue;
-        }
-        if (!strncmp(line, "!model", 6)) {
-            if (line[6] == ' ') {
-                set_prompt_model(line + 7);
-            }
-            printf("Current model: %s\n", get_prompt_model());
-            continue;
-        }
-        if (!strncmp(line, "exit", 4))
-            exit(0);
-
-        while (line && *line != '\n') {
-            char *response = openai_chat("user", line);
-            if (response) {
-                render(response);
-                printf("\n");
-                if (strstr(response, "_STEP_")) {
-                    line = "continue";
-                } else {
-                    line = NULL;
-                }
-                free(response);
-            } else {
-                exit(0);
-            }
-        }
+    if (!strncmp(line, "!dump", 5)) {
+      printf("%s\n", message_json());
+      continue;
     }
+    if (!strncmp(line, "!verbose", 8)) {
+      is_verbose = !is_verbose;
+      fprintf(stderr, "%s\n",
+              is_verbose ? "Verbose mode enabled" : "Verbose mode disabled");
+      continue;
+    }
+    if (line && *line != '\n')
+      line_add_history(line);
+    if (!strncmp(line, "!tools", 6)) {
+      printf("Available tools: %s\n",
+             json_object_to_json_string(tools_descriptions()));
+      continue;
+    }
+    if (!strncmp(line, "!models", 7)) {
+      printf("Current model: %s\n", openai_fetch_models());
+      continue;
+    }
+    if (!strncmp(line, "!model", 6)) {
+      if (line[6] == ' ') {
+        set_prompt_model(line + 7);
+      }
+      printf("Current model: %s\n", get_prompt_model());
+      continue;
+    }
+    if (!strncmp(line, "exit", 4))
+      exit(0);
+
+    while (line && *line != '\n') {
+      char *response = openai_chat("user", line);
+      if (response) {
+        render(response);
+        printf("\n");
+        if (strstr(response, "_STEP_")) {
+          line = "continue";
+        } else {
+          line = NULL;
+        }
+        free(response);
+      } else {
+        exit(0);
+      }
+    }
+  }
 }
 
 static void init(void) {
-    setbuf(stdout, NULL);
-    line_init();
-    auth_init();
-    db_initialize();
-    char *schema = db_get_schema();
-    char payload[1024 * 1024] = {0};
-    snprintf(payload, sizeof(payload),
-            "# LOCAL DATABASE" 
-            "Your have a local database that you can mutate using the query tool and "
-             "the get and set tool."
-             "If you set a value using the tool, make sure that the key is stemmed and lowercased to prevent double entries."
-             "Dialect is sqlite. This is the schema in json format: %s. ",
-             schema);
-    free(schema);
-    fprintf(stderr, "Loading... 📨");
-    openai_system(payload);
-    char * env_system_message = get_env_system_message();
-    if(env_system_message && *env_system_message){
-        openai_system(env_system_message);
-        free(env_system_message);
-    }
-    if (!openai_include(".rcontext.txt")) {
-        openai_include("~/.rcontext.txt");
-    }
-    fprintf(stderr, "\r                          \r");
+  setbuf(stdout, NULL);
+  line_init();
+  auth_init();
+  db_initialize();
+  char *schema = db_get_schema();
+  char payload[1024 * 1024] = {0};
+  snprintf(
+      payload, sizeof(payload),
+      "# LOCAL DATABASE"
+      "Your have a local database that you can mutate using the query tool and "
+      "the get and set tool."
+      "If you set a value using the tool, make sure that the key is stemmed "
+      "and lowercased to prevent double entries."
+      "Dialect is sqlite. This is the schema in json format: %s. ",
+      schema);
+  free(schema);
+  fprintf(stderr, "Loading... 📨");
+  openai_system(payload);
+  char *env_system_message = get_env_system_message();
+  if (env_system_message && *env_system_message) {
+    openai_system(env_system_message);
+    free(env_system_message);
+  }
+  if (!openai_include(".rcontext.txt")) {
+    openai_include("~/.rcontext.txt");
+  }
+  fprintf(stderr, "\r                          \r");
 }
 
 static void handle_sigint(int sig) {
-    time_t current_time = time(NULL);
-    printf("\n");
-    if (sigint_count == 0) {
-        first_sigint_time = current_time;
-        sigint_count++;
+  time_t current_time = time(NULL);
+  printf("\n");
+  if (sigint_count == 0) {
+    first_sigint_time = current_time;
+    sigint_count++;
+  } else {
+    if (difftime(current_time, first_sigint_time) <= 1) {
+      exit(0);
     } else {
-        if (difftime(current_time, first_sigint_time) <= 1) {
-            exit(0);
-        } else {
-            sigint_count = 1;
-            first_sigint_time = current_time;
-        }
+      sigint_count = 1;
+      first_sigint_time = current_time;
     }
+  }
 }
 
 int main(int argc, char *argv[]) {
-    signal(SIGINT, handle_sigint);
+  signal(SIGINT, handle_sigint);
 
-    init();
-    char * env_string = get_env_string();
-    if(env_string && *env_string){
-        openai_system(env_string);
-        free(env_string);
-    }
-    if (try_prompt(argc, argv))
-        return 0;
-
-    repl();
+  init();
+  char *env_string = get_env_string();
+  if (env_string && *env_string) {
+    openai_system(env_string);
+    free(env_string);
+  }
+  if (try_prompt(argc, argv))
     return 0;
+
+  repl();
+  return 0;
 }
diff --git a/markdown.h b/markdown.h
index 97709f9..46ec120 100644
--- a/markdown.h
+++ b/markdown.h
@@ -1,45 +1,30 @@
-// Written by retoor@molodetz.nl
-
-// This program provides functionality to highlight the keywords in source code
-// using ANSI color formatting and convert Markdown syntax into ANSI-colored
-// text output.
-
-// Uses standard C libraries: <stdio.h>, <string.h>. Also utilizes ANSI escape
-// codes for text formatting.
-
-// MIT License:
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-//
-// The above copyright notice and this permission notice shall be included in
-// all copies or substantial portions of the Software.
-//
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-
+#include <ctype.h>
 #include <stdbool.h>
 #include <stdio.h>
 #include <string.h>
 
+// --- ANSI Escape Codes ---
 #define RESET "\033[0m"
 #define BOLD "\033[1m"
 #define ITALIC "\033[3m"
+#define STRIKETHROUGH "\033[9m"
+
 #define FG_YELLOW "\033[33m"
 #define FG_BLUE "\033[34m"
 #define FG_CYAN "\033[36m"
+#define FG_MAGENTA "\033[35m"
 
+#define BG_YELLOW_FG_BLACK "\033[43;30m"
+
+/**
+ * @brief Checks if a given word is a programming language keyword.
+ * * @param word The word to check.
+ * @return int 1 if it's a keyword, 0 otherwise.
+ */
 int is_keyword(const char *word) {
-
+  // A comprehensive list of keywords from various popular languages.
   const char *keywords[] = {
+      // C keywords
       "int", "float", "double", "char", "void", "if", "else", "while", "for",
       "return", "struct", "printf",
       // Rust keywords
@@ -75,33 +60,38 @@ int is_keyword(const char *word) {
   return 0;
 }
 
+/**
+ * @brief Applies basic syntax highlighting to a string of code.
+ * * @param code The code string to highlight.
+ */
 void highlight_code(const char *code) {
   const char *ptr = code;
   char buffer[4096];
   size_t index = 0;
 
   while (*ptr) {
-    if ((*ptr >= 'a' && *ptr <= 'z') || (*ptr >= 'A' && *ptr <= 'Z') ||
-        (*ptr == '_')) {
-      while ((*ptr >= 'a' && *ptr <= 'z') || (*ptr >= 'A' && *ptr <= 'Z') ||
-             (*ptr >= '0' && *ptr <= '9') || (*ptr == '_')) {
+    // Highlight keywords
+    if (isalpha((unsigned char)*ptr) || *ptr == '_') {
+      while (isalnum((unsigned char)*ptr) || *ptr == '_') {
         buffer[index++] = *ptr++;
       }
-      buffer[index] = 0;
+      buffer[index] = '\0';
 
       if (is_keyword(buffer)) {
-        printf(FG_BLUE "%s" RESET, buffer);
+        printf(FG_BLUE "%s" RESET FG_YELLOW, buffer);
       } else {
         printf("%s", buffer);
       }
       index = 0;
-    } else if (*ptr >= '0' && *ptr <= '9') {
-      while (*ptr >= '0' && *ptr <= '9') {
+      // Highlight numbers
+    } else if (isdigit((unsigned char)*ptr)) {
+      while (isdigit((unsigned char)*ptr)) {
         buffer[index++] = *ptr++;
       }
-      buffer[index] = 0;
-      printf(FG_CYAN "%s" RESET, buffer);
+      buffer[index] = '\0';
+      printf(FG_CYAN "%s" RESET FG_YELLOW, buffer);
       index = 0;
+      // Print other characters as-is
     } else {
       putchar(*ptr);
       ptr++;
@@ -109,93 +99,253 @@ void highlight_code(const char *code) {
   }
 }
 
+/**
+ * @brief Parses a Markdown string and prints it to the console with ANSI color
+ * codes.
+ *
+ * This version supports a wide range of Markdown features, including:
+ * - Headers (H1-H6)
+ * - Bold (**, __) and Italic (*, _) text
+ * - Strikethrough (~~) and Highlight (==)
+ * - Blockquotes (>), Nested Ordered (1.) and Unordered lists (*, -, +)
+ * - Inline code (`) and full code blocks (```) with syntax highlighting
+ * - Links ([text](url)) and Horizontal rules (---, ***)
+ * * @param markdown The raw Markdown string to parse.
+ */
 void parse_markdown_to_ansi(const char *markdown) {
   const char *ptr = markdown;
-  bool inside_code = false;
+  bool is_start_of_line = true;
 
   while (*ptr) {
-    if (*ptr == '`' && *(ptr + 1) != '`') {
-      inside_code = !inside_code;
-      if (inside_code) {
+    // --- Code Blocks (```) ---
+    if (is_start_of_line && strncmp(ptr, "```", 3) == 0) {
+      ptr += 3;
+      while (*ptr && *ptr != '\n')
+        ptr++;
+      if (*ptr)
+        ptr++;
+
+      const char *code_start = ptr;
+      const char *code_end = strstr(code_start, "```");
+
+      if (code_end) {
+        char block_buffer[code_end - code_start + 1];
+        strncpy(block_buffer, code_start, code_end - code_start);
+        block_buffer[code_end - code_start] = '\0';
+
         printf(FG_YELLOW);
-      } else {
+        highlight_code(block_buffer);
         printf(RESET);
-      }
-      ptr++;
-      continue;
-    } else if (!strncmp(ptr, "```", 3)) {
-      inside_code = !inside_code;
-      if (inside_code) {
-        ptr = strstr(ptr, "\n") + 1;
+
+        ptr = code_end + 3;
+        if (*ptr == '\n')
+          ptr++;
+        is_start_of_line = true;
+        continue;
       } else {
-        ptr += 3;
-      }
-      if (*ptr == '\0') {
+        printf(FG_YELLOW);
+        highlight_code(code_start);
+        printf(RESET);
         break;
       }
     }
 
-    if (inside_code) {
-      char code_buffer[1024 * 1024] = {0};
-      ;
-      size_t index = 0;
-
-      while (*ptr && *ptr != '`') {
-        code_buffer[index++] = *ptr++;
-        if (*ptr == '\n' || *ptr == ' ' || *ptr == '\t' || *ptr == '.') {
-          code_buffer[index++] = 0;
-          highlight_code(code_buffer);
-          index = 0;
-        }
-      }
-      code_buffer[index] = 0;
-      if (index) {
-        highlight_code(code_buffer);
-      }
-    } else {
-      if (strncmp(ptr, "**", 2) == 0) {
-        printf(BOLD);
-        ptr += 2;
-        while (*ptr && strncmp(ptr, "**", 2) != 0) {
-          putchar(*ptr++);
-        }
-        if (*ptr == '*' && *(ptr + 1) == '*')
-          ptr += 2;
-        printf(RESET);
-      } else if (*ptr == '*' && (ptr == markdown || *(ptr - 1) != '*')) {
-        printf(ITALIC);
+    // --- Block-level Elements (checked at the start of a line) ---
+    if (is_start_of_line) {
+      const char *line_start_ptr = ptr;
+      int indent_level = 0;
+      while (*ptr == ' ') {
+        indent_level++;
         ptr++;
-        while (*ptr && *ptr != '*') {
-          putchar(*ptr++);
-        }
-        if (*ptr == '*')
-          ptr++;
-        printf(RESET);
+      }
+
+      bool block_processed = true;
+      if (strncmp(ptr, "###### ", 7) == 0) {
+        printf(BOLD FG_YELLOW);
+        ptr += 7;
+      } else if (strncmp(ptr, "##### ", 6) == 0) {
+        printf(BOLD FG_YELLOW);
+        ptr += 6;
+      } else if (strncmp(ptr, "#### ", 5) == 0) {
+        printf(BOLD FG_YELLOW);
+        ptr += 5;
       } else if (strncmp(ptr, "### ", 4) == 0) {
         printf(BOLD FG_YELLOW);
         ptr += 4;
-        while (*ptr && *ptr != '\n') {
-          putchar(*ptr++);
-        }
-        printf(RESET "\n");
       } else if (strncmp(ptr, "## ", 3) == 0) {
         printf(BOLD FG_YELLOW);
         ptr += 3;
-        while (*ptr && *ptr != '\n') {
-          putchar(*ptr++);
-        }
-        printf(RESET "\n");
       } else if (strncmp(ptr, "# ", 2) == 0) {
         printf(BOLD FG_YELLOW);
         ptr += 2;
-        while (*ptr && *ptr != '\n') {
-          putchar(*ptr++);
-        }
-        printf(RESET "\n");
+      } else if ((strncmp(ptr, "---", 3) == 0 || strncmp(ptr, "***", 3) == 0) &&
+                 (*(ptr + 3) == '\n' || *(ptr + 3) == '\0')) {
+        printf(FG_CYAN "───────────────────────────────────────────────────────"
+                       "──────────" RESET "\n");
+        ptr += 3;
+        if (*ptr == '\n')
+          ptr++;
+        is_start_of_line = true;
+        continue;
+      } else if (strncmp(ptr, "> ", 2) == 0) {
+        for (int i = 0; i < indent_level; i++)
+          putchar(' ');
+        printf(ITALIC FG_CYAN "▎ " RESET);
+        ptr += 2;
+        is_start_of_line = false;
+        continue;
+      } else if ((*ptr == '*' || *ptr == '-' || *ptr == '+') &&
+                 *(ptr + 1) == ' ') {
+        for (int i = 0; i < indent_level; i++)
+          putchar(' ');
+        printf(FG_MAGENTA "• " RESET);
+        ptr += 2;
+        is_start_of_line = false;
+        continue;
       } else {
-        putchar(*ptr);
-        ptr++;
+        const char *temp_ptr = ptr;
+        while (isdigit((unsigned char)*temp_ptr))
+          temp_ptr++;
+        if (temp_ptr > ptr && *temp_ptr == '.' && *(temp_ptr + 1) == ' ') {
+          for (int i = 0; i < indent_level; i++)
+            putchar(' ');
+          printf(FG_MAGENTA);
+          fwrite(ptr, 1, (temp_ptr - ptr) + 1, stdout);
+          printf(" " RESET);
+          ptr = temp_ptr + 2;
+          is_start_of_line = false;
+          continue;
+        } else {
+          block_processed = false;
+          ptr = line_start_ptr;
+        }
+      }
+      if (block_processed) {
+        while (*ptr && *ptr != '\n')
+          putchar(*ptr++);
+        printf(RESET "\n");
+        if (*ptr == '\n')
+          ptr++;
+        is_start_of_line = true;
+        continue;
       }
     }
+
+    // --- Inline Elements (order is important) ---
+    if (strncmp(ptr, "***", 3) == 0 || strncmp(ptr, "___", 3) == 0) {
+      const char *marker = strncmp(ptr, "***", 3) == 0 ? "***" : "___";
+      printf(BOLD ITALIC);
+      ptr += 3;
+      const char *end = strstr(ptr, marker);
+      if (end) {
+        fwrite(ptr, 1, end - ptr, stdout);
+        ptr = end + 3;
+      } else {
+        fputs(ptr, stdout);
+        ptr += strlen(ptr);
+      }
+      printf(RESET);
+      continue;
+    }
+    if (strncmp(ptr, "**", 2) == 0 || strncmp(ptr, "__", 2) == 0) {
+      const char *marker = strncmp(ptr, "**", 2) == 0 ? "**" : "__";
+      printf(BOLD);
+      ptr += 2;
+      const char *end = strstr(ptr, marker);
+      if (end) {
+        fwrite(ptr, 1, end - ptr, stdout);
+        ptr = end + 2;
+      } else {
+        fputs(ptr, stdout);
+        ptr += strlen(ptr);
+      }
+      printf(RESET);
+      continue;
+    }
+    if ((*ptr == '*' || *ptr == '_') && !isspace(*(ptr - 1)) &&
+        !isspace(*(ptr + 1))) {
+      char marker = *ptr;
+      printf(ITALIC);
+      ptr++;
+      const char *start = ptr;
+      while (*ptr && *ptr != marker)
+        ptr++;
+      if (*ptr == marker) {
+        fwrite(start, 1, ptr - start, stdout);
+        ptr++;
+      } else {
+        putchar(marker);
+        ptr = start;
+      }
+      printf(RESET);
+      continue;
+    }
+    if (strncmp(ptr, "~~", 2) == 0) {
+      printf(STRIKETHROUGH);
+      ptr += 2;
+      const char *end = strstr(ptr, "~~");
+      if (end) {
+        fwrite(ptr, 1, end - ptr, stdout);
+        ptr = end + 2;
+      } else {
+        fputs(ptr, stdout);
+        ptr += strlen(ptr);
+      }
+      printf(RESET);
+      continue;
+    }
+    if (strncmp(ptr, "==", 2) == 0) {
+      printf(BG_YELLOW_FG_BLACK);
+      ptr += 2;
+      const char *end = strstr(ptr, "==");
+      if (end) {
+        fwrite(ptr, 1, end - ptr, stdout);
+        ptr = end + 2;
+      } else {
+        fputs(ptr, stdout);
+        ptr += strlen(ptr);
+      }
+      printf(RESET);
+      continue;
+    }
+    if (*ptr == '`' && *(ptr + 1) != '`') {
+      printf(FG_YELLOW);
+      ptr++;
+      const char *start = ptr;
+      while (*ptr && *ptr != '`')
+        ptr++;
+      fwrite(start, 1, ptr - start, stdout);
+      if (*ptr == '`')
+        ptr++;
+      printf(RESET);
+      continue;
+    }
+    if (*ptr == '[') {
+      const char *text_start = ptr + 1;
+      const char *text_end = strchr(text_start, ']');
+      if (text_end && *(text_end + 1) == '(') {
+        const char *url_start = text_end + 2;
+        const char *url_end = strchr(url_start, ')');
+        if (url_end) {
+          printf(FG_BLUE);
+          fwrite(text_start, 1, text_end - text_start, stdout);
+          printf(RESET " (");
+          printf(ITALIC FG_CYAN);
+          fwrite(url_start, 1, url_end - url_start, stdout);
+          printf(RESET ")");
+          ptr = url_end + 1;
+          continue;
+        }
+      }
+    }
+
+    // --- Default Character ---
+    if (*ptr == '\n') {
+      is_start_of_line = true;
+    } else if (!isspace((unsigned char)*ptr)) {
+      is_start_of_line = false;
+    }
+    putchar(*ptr);
+    ptr++;
   }
 }
diff --git a/messages.h b/messages.h
old mode 100644
new mode 100755
diff --git a/openai.h b/openai.h
old mode 100644
new mode 100755
diff --git a/plugin.h b/plugin.h
old mode 100644
new mode 100755
diff --git a/r.desktop b/r.desktop
old mode 100644
new mode 100755
diff --git a/r.h b/r.h
index 321cd75..ef639d8 100644
--- a/r.h
+++ b/r.h
@@ -32,31 +32,30 @@ char *_model = NULL;
 #define DB_FILE "~/.r.db"
 #define PROMPT_TEMPERATURE 0.1
 
-
-bool use_tools(){
-    if(getenv("R_USE_TOOLS") != NULL){
-        const char *value = getenv("R_USE_TOOLS");
-        if (!strcmp(value, "true")) {
-            return true;
-        }
-        if (!strcmp(value, "false")) {
-            return false;
-        }
-        if (!strcmp(value, "1")) {
-            return true;
-        }
-        if (!strcmp(value, "0")) {
-            return false;
-        }
+bool use_tools() {
+  if (getenv("R_USE_TOOLS") != NULL) {
+    const char *value = getenv("R_USE_TOOLS");
+    if (!strcmp(value, "true")) {
+      return true;
     }
-    return true;
+    if (!strcmp(value, "false")) {
+      return false;
+    }
+    if (!strcmp(value, "1")) {
+      return true;
+    }
+    if (!strcmp(value, "0")) {
+      return false;
+    }
+  }
+  return true;
 }
 
-char * get_env_system_message(){
-    if (getenv("R_SYSTEM_MESSAGE") != NULL) {
-        return strdup(getenv("R_SYSTEM_MESSAGE"));
-    }
-    return NULL;
+char *get_env_system_message() {
+  if (getenv("R_SYSTEM_MESSAGE") != NULL) {
+    return strdup(getenv("R_SYSTEM_MESSAGE"));
+  }
+  return NULL;
 }
 
 bool get_use_strict() {
diff --git a/r.png b/r.png
old mode 100644
new mode 100755
diff --git a/review.md b/review.md
old mode 100644
new mode 100755
diff --git a/rpylib.c b/rpylib.c
old mode 100644
new mode 100755
diff --git a/screenshot1.png b/screenshot1.png
old mode 100644
new mode 100755
diff --git a/setup.py b/setup.py
old mode 100644
new mode 100755
diff --git a/tools.h b/tools.h
index 366e8d2..452294b 100644
--- a/tools.h
+++ b/tools.h
@@ -56,7 +56,6 @@ struct json_object *tool_description_rag_chunk();
 char *tool_function_rag_search(char *query, int top_k);
 char *tool_function_rag_chunk(char *file_path);
 
-
 char *tool_function_python_execute(char *source_code);
 
 struct json_object *tools_descriptions() {
@@ -66,7 +65,7 @@ struct json_object *tools_descriptions() {
   json_object_array_add(root, tool_description_directory_glob());
   json_object_array_add(root, tool_description_read_file());
   json_object_array_add(root, tool_description_write_file());
-  //json_object_array_add(root, tool_description_directory_rglob());
+  // json_object_array_add(root, tool_description_directory_rglob());
   json_object_array_add(root, tool_description_linux_terminal_interactive());
   json_object_array_add(root, tool_description_index_source_directory());
   json_object_array_add(root, tool_description_chdir());
@@ -424,81 +423,88 @@ char *tool_function_linux_terminal_interactive(char *command) {
 
 // ---- PYTHON EXECUTE TOOL ----
 char *tool_function_python_execute(char *source_code) {
-    char tmp_file[] = "/tmp/r_python_tool_XXXXXX.py";
-    int fd = mkstemps(tmp_file, 3); // 3 for ".py"
-    if (fd == -1) {
-        return strdup("Failed to create temporary file for Python code.");
-    }
-    FILE *fp = fdopen(fd, "w");
-    if (!fp) {
-        close(fd);
-        return strdup("Failed to open temporary file for writing.");
-    }
-    fwrite(source_code, 1, strlen(source_code), fp);
-    fclose(fp);
+  char tmp_file[] = "/tmp/r_python_tool_XXXXXX.py";
+  int fd = mkstemps(tmp_file, 3); // 3 for ".py"
+  if (fd == -1) {
+    return strdup("Failed to create temporary file for Python code.");
+  }
+  FILE *fp = fdopen(fd, "w");
+  if (!fp) {
+    close(fd);
+    return strdup("Failed to open temporary file for writing.");
+  }
+  fwrite(source_code, 1, strlen(source_code), fp);
+  fclose(fp);
 
-    char command[4096];
-    snprintf(command, sizeof(command), "python3 '%s' 2>&1", tmp_file);
+  char command[4096];
+  snprintf(command, sizeof(command), "python3 '%s' 2>&1", tmp_file);
 
-    FILE *proc = popen(command, "r");
-    if (!proc) {
-        unlink(tmp_file);
-        return strdup("Failed to execute python3.");
-    }
-    char buffer[1024];
-    size_t total = 0;
-    char *output = NULL;
-    while (fgets(buffer, sizeof(buffer), proc)) {
-        size_t len = strlen(buffer);
-        char *new_output = realloc(output, total + len + 1);
-        if (!new_output) {
-            free(output);
-            pclose(proc);
-            unlink(tmp_file);
-            return strdup("Memory allocation failed.");
-        }
-        output = new_output;
-        strcpy(output + total, buffer);
-        total += len;
-    }
-    if (output)
-        output[total] = 0;
-    else
-        output = strdup("");
-    pclose(proc);
+  FILE *proc = popen(command, "r");
+  if (!proc) {
     unlink(tmp_file);
-    return output;
+    return strdup("Failed to execute python3.");
+  }
+  char buffer[1024];
+  size_t total = 0;
+  char *output = NULL;
+  while (fgets(buffer, sizeof(buffer), proc)) {
+    size_t len = strlen(buffer);
+    char *new_output = realloc(output, total + len + 1);
+    if (!new_output) {
+      free(output);
+      pclose(proc);
+      unlink(tmp_file);
+      return strdup("Memory allocation failed.");
+    }
+    output = new_output;
+    strcpy(output + total, buffer);
+    total += len;
+  }
+  if (output)
+    output[total] = 0;
+  else
+    output = strdup("");
+  pclose(proc);
+  unlink(tmp_file);
+  return output;
 }
 
 struct json_object *tool_description_python_execute() {
-    struct json_object *root = json_object_new_object();
-    json_object_object_add(root, "type", json_object_new_string("function"));
+  struct json_object *root = json_object_new_object();
+  json_object_object_add(root, "type", json_object_new_string("function"));
 
-    struct json_object *function = json_object_new_object();
-    json_object_object_add(function, "name", json_object_new_string("python_execute"));
-    json_object_object_add(function, "description", json_object_new_string("Executes Python source code using the python3 interpreter and returns stdout/stderr."));
+  struct json_object *function = json_object_new_object();
+  json_object_object_add(function, "name",
+                         json_object_new_string("python_execute"));
+  json_object_object_add(
+      function, "description",
+      json_object_new_string("Executes Python source code using the python3 "
+                             "interpreter and returns stdout/stderr."));
 
-    struct json_object *parameters = json_object_new_object();
-    json_object_object_add(parameters, "type", json_object_new_string("object"));
+  struct json_object *parameters = json_object_new_object();
+  json_object_object_add(parameters, "type", json_object_new_string("object"));
 
-    struct json_object *properties = json_object_new_object();
-    struct json_object *source = json_object_new_object();
-    json_object_object_add(source, "type", json_object_new_string("string"));
-    json_object_object_add(source, "description", json_object_new_string("Python source code to execute."));
-    json_object_object_add(properties, "source", source);
+  struct json_object *properties = json_object_new_object();
+  struct json_object *source = json_object_new_object();
+  json_object_object_add(source, "type", json_object_new_string("string"));
+  json_object_object_add(
+      source, "description",
+      json_object_new_string("Python source code to execute."));
+  json_object_object_add(properties, "source", source);
 
-    json_object_object_add(parameters, "properties", properties);
+  json_object_object_add(parameters, "properties", properties);
 
-    struct json_object *required = json_object_new_array();
-    json_object_array_add(required, json_object_new_string("source"));
-    json_object_object_add(parameters, "required", required);
+  struct json_object *required = json_object_new_array();
+  json_object_array_add(required, json_object_new_string("source"));
+  json_object_object_add(parameters, "required", required);
 
-    json_object_object_add(parameters, "additionalProperties", json_object_new_boolean(0));
-    json_object_object_add(function, "parameters", parameters);
+  json_object_object_add(parameters, "additionalProperties",
+                         json_object_new_boolean(0));
+  json_object_object_add(function, "parameters", parameters);
 
-    json_object_object_add(root, "function", function);
+  json_object_object_add(root, "function", function);
 
-    return root;
+  return root;
 }
 // ---- END PYTHON EXECUTE TOOL ----
 
@@ -646,9 +652,10 @@ struct json_object *tool_description_linux_terminal_interactive() {
   struct json_object *properties = json_object_new_object();
   struct json_object *path = json_object_new_object();
   json_object_object_add(path, "type", json_object_new_string("string"));
-  json_object_object_add(path, "description",
-                         json_object_new_string(
-                             "Executable with parameters to execute interactively."));
+  json_object_object_add(
+      path, "description",
+      json_object_new_string(
+          "Executable with parameters to execute interactively."));
   json_object_object_add(properties, "command", path);
 
   json_object_object_add(parameters, "properties", properties);
@@ -672,7 +679,7 @@ struct json_object *tool_description_linux_terminal_interactive() {
 }
 
 struct json_object *tool_description_directory_rglob() {
-    
+
   struct json_object *root = json_object_new_object();
   json_object_object_add(root, "type", json_object_new_string("function"));
 
@@ -816,9 +823,9 @@ struct json_object *tool_description_write_file() {
 }
 
 char *tool_function_index_source_directory(char *path) {
-  char * result = index_directory(path);
-  if(!result)
-      return strdup("Failed to index directory!");
+  char *result = index_directory(path);
+  if (!result)
+    return strdup("Failed to index directory!");
   return result;
 }
 
@@ -1207,33 +1214,32 @@ struct json_object *tool_description_linux_terminal() {
 }
 
 char *tool_function_mkdir(char *path) {
-    char temp[2048];
-    char *p = NULL;
-    size_t len;
+  char temp[2048];
+  char *p = NULL;
+  size_t len;
 
-    snprintf(temp, sizeof(temp), "%s", path);
-    len = strlen(temp);
+  snprintf(temp, sizeof(temp), "%s", path);
+  len = strlen(temp);
 
-    if (temp[len - 1] == '/') {
-        temp[len - 1] = '\0';
-    }
+  if (temp[len - 1] == '/') {
+    temp[len - 1] = '\0';
+  }
 
-    for (p = temp + 1; *p; p++) {
-        if (*p == '/') {
-            *p = '\0';
-            if (mkdir(temp, 0777) != 0 && errno != EEXIST) {
-                return strdup("Failed to create directory!");
-            }
-            *p = '/';
-        }
-    }
-    if (mkdir(temp, 0777) != 0 && errno != EEXIST) {
+  for (p = temp + 1; *p; p++) {
+    if (*p == '/') {
+      *p = '\0';
+      if (mkdir(temp, 0777) != 0 && errno != EEXIST) {
         return strdup("Failed to create directory!");
+      }
+      *p = '/';
     }
-    return strdup("Directory successfully created.");
+  }
+  if (mkdir(temp, 0777) != 0 && errno != EEXIST) {
+    return strdup("Failed to create directory!");
+  }
+  return strdup("Directory successfully created.");
 }
 
-
 struct json_object *tool_description_mkdir() {
   struct json_object *root = json_object_new_object();
   json_object_object_add(root, "type", json_object_new_string("function"));
@@ -1562,15 +1568,18 @@ struct json_object *tools_execute(struct json_object *tools_array) {
         }
       } else if (!strcmp(function_name, "python_execute")) {
         struct json_object *arguments_obj;
-        if (json_object_object_get_ex(function_obj, "arguments", &arguments_obj)) {
-            struct json_object *arguments = json_tokener_parse(json_object_get_string(arguments_obj));
-            struct json_object *source_obj;
-            if (json_object_object_get_ex(arguments, "source", &source_obj)) {
-                char *source = (char *)json_object_get_string(source_obj);
-                char *result = tool_function_python_execute(source);
-                json_object_object_add(tool_result, "content", json_object_new_string(result));
-                free(result);
-            }
+        if (json_object_object_get_ex(function_obj, "arguments",
+                                      &arguments_obj)) {
+          struct json_object *arguments =
+              json_tokener_parse(json_object_get_string(arguments_obj));
+          struct json_object *source_obj;
+          if (json_object_object_get_ex(arguments, "source", &source_obj)) {
+            char *source = (char *)json_object_get_string(source_obj);
+            char *result = tool_function_python_execute(source);
+            json_object_object_add(tool_result, "content",
+                                   json_object_new_string(result));
+            free(result);
+          }
         }
       } else {
         fprintf(stderr, "Unknown function: %s\n", function_name);
diff --git a/url.h b/url.h
old mode 100644
new mode 100755
diff --git a/utils.h b/utils.h
old mode 100644
new mode 100755