diff --git a/TODO.md b/TODO.md
index de3a960..1501a29 100644
--- a/TODO.md
+++ b/TODO.md
@@ -1,7 +1,4 @@
 # TODO
-- [x] Cache html version until changes in md file  
+- [ ] Adding user authentications for restricted access
 - [ ] Optional auth to protect files against changes by unauthorized users
-- [x] Edit and remove icons at the top instead of the text at the bottom
-- [ ] Drawio integration
-- [x] Knowledge graph using [visjs](https://visjs.github.io/vis-network/examples/)
-- [x] use better search mechanism, using [whoosh](https://whoosh.readthedocs.io/en/latest/intro.html)
+- [ ] Drawio integration
\ No newline at end of file
diff --git a/config.py b/config.py
deleted file mode 100644
index 83b4363..0000000
--- a/config.py
+++ /dev/null
@@ -1,107 +0,0 @@
-import os
-import yaml
-
-WIKMD_CONFIG_FILE = "wikmd-config.yaml"
-
-# Default config parameters
-WIKMD_HOST_DEFAULT = "0.0.0.0"
-WIKMD_PORT_DEFAULT = 5000
-WIKMD_LOGGING_DEFAULT = 1
-WIKMD_LOGGING_FILE_DEFAULT = "wikmd.log"
-
-GIT_EMAIL_DEFAULT = "wikmd@no-mail.com"
-GIT_USER_DEFAULT = "wikmd"
-
-MAIN_BRANCH_NAME_DEFAULT = "main"
-SYNC_WITH_REMOTE_DEFAULT = 0
-REMOTE_URL_DEFAULT = ""
-
-WIKI_DIRECTORY_DEFAULT = "wiki"
-HOMEPAGE_DEFAULT = "homepage.md"
-HOMEPAGE_TITLE_DEFAULT = "homepage"
-IMAGES_ROUTE_DEFAULT = "img"
-
-HIDE_FOLDER_IN_WIKI = []
-
-PLUGINS = []
-
-PROTECT_EDIT_BY_PASSWORD = 0
-PASSWORD_IN_SHA_256 = "0E9C700FAB2D5B03B0581D080E74A2D7428758FC82BD423824C6C11D6A7F155E" #pw: wikmd
-
-# if False: Uses external CDNs to serve some files
-LOCAL_MODE = False
-
-IMAGE_ALLOWED_MIME_DEFAULT = ["image/gif", "image/jpeg", "image/png", "image/svg+xml", "image/webp"]
-# you need to have cwebp installed for optimization to work
-OPTIMIZE_IMAGES_DEFAULT = "no"
-
-CACHE_DIR = "/dev/shm/wikmd/cache"
-SEARCH_DIR = "/dev/shm/wikmd/searchindex"
-
-SECRET_KEY = '\xfd{H\xe5<\x95\xf9\xe3\x96.5\xd1\x01O<!\xd5\xa2\xa0\x9fR"\xa1\xa8'
-
-def config_list(yaml_config, config_item_name, default_value):
-    """
-    Function that gets a config item of type list.
-    Priority is in the following order either from environment variables or yaml file or default value.
-    """
-    if os.getenv(config_item_name.upper()):
-        # Env Var in the form `EXAMPLE="a, b, c, d"` or `EXAMPLE="a,b,c,d"`
-        return [ext.strip() for ext in os.getenv(config_item_name.upper()).split(",")]
-    elif yaml_config[config_item_name.lower()]:
-        return yaml_config[config_item_name.lower()]
-    else:
-        return default_value
-
-
-class WikmdConfig:
-    """
-    Class that stores the configuration of wikmd.
-    """
-    def __init__(self):
-        """
-        Function that gets the configuration parameters from .yaml file, os environment variables or default values.
-        Each configuration parameter is stored into a class attribute.
-        Env. vars take precedence.
-        """
-        __location__ = os.path.realpath(
-            os.path.join(os.getcwd(), os.path.dirname(__file__)))
-
-        # .yaml config file
-        with open(os.path.join(__location__, WIKMD_CONFIG_FILE)) as f:
-            yaml_config = yaml.safe_load(f)
-
-        # Load config parameters from env. vars, yaml or default values (the firsts take precedence)
-        self.wikmd_host = os.getenv("WIKMD_HOST") or yaml_config.get("wikmd_host", WIKMD_HOST_DEFAULT)
-        self.wikmd_port = os.getenv("WIKMD_PORT") or yaml_config.get("wikmd_port", WIKMD_PORT_DEFAULT)
-        self.wikmd_logging = os.getenv("WIKMD_LOGGING") or yaml_config.get("wikmd_logging", WIKMD_LOGGING_DEFAULT)
-        self.wikmd_logging_file = os.getenv("WIKMD_LOGGING_FILE") or yaml_config.get("wikmd_logging_file", WIKMD_LOGGING_FILE_DEFAULT)
-
-        self.git_user = os.getenv("GIT_USER") or yaml_config.get("git_user", GIT_USER_DEFAULT)
-        self.git_email = os.getenv("GIT_EMAIL") or yaml_config.get("git_emai", GIT_EMAIL_DEFAULT)
-
-        self.main_branch_name = os.getenv("MAIN_BRANCH_NAME") or yaml_config.get("main_branch_name", MAIN_BRANCH_NAME_DEFAULT)
-        self.sync_with_remote = os.getenv("SYNC_WITH_REMOTE") or yaml_config.get("sync_with_remote", SYNC_WITH_REMOTE_DEFAULT)
-        self.remote_url = os.getenv("REMOTE_URL") or yaml_config.get("remote_url", REMOTE_URL_DEFAULT)
-
-        self.wiki_directory = os.getenv("WIKI_DIRECTORY") or yaml_config.get("wiki_directory", WIKI_DIRECTORY_DEFAULT)
-        self.homepage = os.getenv("HOMEPAGE") or yaml_config.get("homepage", HOMEPAGE_DEFAULT)
-        self.homepage_title = os.getenv("HOMEPAGE_TITLE") or yaml_config.get("homepage_title", HOMEPAGE_TITLE_DEFAULT)
-        self.images_route = os.getenv("IMAGES_ROUTE") or yaml_config.get("images_route", IMAGES_ROUTE_DEFAULT)
-
-        self.hide_folder_in_wiki = os.getenv("HIDE_FOLDER_IN_WIKI") or yaml_config.get("hide_folder_in_wiki", HIDE_FOLDER_IN_WIKI)
-
-        self.plugins = os.getenv("WIKI_PLUGINS") or yaml_config.get("plugins", PLUGINS)
-
-        self.protect_edit_by_password = os.getenv("PROTECT_EDIT_BY_PASSWORD") or yaml_config.get("protect_edit_by_password", PROTECT_EDIT_BY_PASSWORD)
-        self.password_in_sha_256 = os.getenv("PASSWORD_IN_SHA_256") or yaml_config.get("password_in_sha_256", PASSWORD_IN_SHA_256)
-
-        self.local_mode = (os.getenv("LOCAL_MODE") in ["True", "true", "Yes", "yes"]) or yaml_config.get("local_mode", LOCAL_MODE)
-
-        self.image_allowed_mime = config_list(yaml_config, "IMAGE_ALLOWED_MIME", IMAGE_ALLOWED_MIME_DEFAULT)
-        self.optimize_images = os.getenv("OPTIMIZE_IMAGES") or yaml_config.get("optimize_images", OPTIMIZE_IMAGES_DEFAULT)
-
-        self.cache_dir = os.getenv("CACHE_DIR") or yaml_config.get("cache_dir", CACHE_DIR)
-        self.search_dir = os.getenv("SEARCH_DIR") or yaml_config.get("search_dir", SEARCH_DIR)
-
-        self.secret_key = os.getenv("SECRET_KEY") or yaml_config.get("secret_key", SECRET_KEY)
diff --git a/wikmd-config.yaml b/config.yaml
similarity index 89%
rename from wikmd-config.yaml
rename to config.yaml
index e2d6092..59e46b7 100644
--- a/wikmd-config.yaml
+++ b/config.yaml
@@ -3,10 +3,10 @@
 wikmd_host: "0.0.0.0"
 wikmd_port: 5000
 wikmd_logging: 1
-wikmd_logging_file: "wikmd.log"
+wikmd_logging_file: "wikimd.log"
 
-git_user: "wikmd"
-git_email: "wikmd@no-mail.com"
+git_user: "wikimd"
+git_email: "wikimd@no-mail.com"
 
 main_branch_name: "main"
 sync_with_remote: 0
diff --git a/requirements.txt b/requirements.txt
index 7b25c49..34fc54a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,26 +1,32 @@
+beautifulsoup4==4.12.3
+blinker==1.7.0
+cachelib==0.12.0
+certifi==2024.2.2
+charset-normalizer==3.3.2
+click==8.1.7
 Flask==3.0.2
+Flask-Login==0.6.3
+gitdb==4.0.11
 GitPython==3.1.42
+idna==3.6
 itsdangerous==2.1.2
 Jinja2==3.1.3
+lxml==5.1.0
 Markdown==3.5.2
 MarkupSafe==2.1.5
-PyYAML==6.0.1
-Werkzeug==3.0.1
-Whoosh==2.7.4
-beautifulsoup4==4.12.3
-click==8.1.7
-gitdb==4.0.11
-idna==3.6
 pandoc-eqnos==2.5.0
 pandoc-fignos==2.4.0
 pandoc-secnos==2.2.2
 pandoc-tablenos==2.3.0
 pandoc-xnos==2.5.0
 pandocfilters==1.5.1
+psutil==5.9.8
 pypandoc==1.13
+PyYAML==6.0.1
 requests==2.31.0
 smmap==5.0.1
-lxml==5.1.0
+soupsieve==2.5
+urllib3==2.2.1
 watchdog==2.1.9
-cachelib==0.12.0
-psutil==5.9.8
+Werkzeug==3.0.1
+Whoosh==2.7.4
diff --git a/__init__.py b/src/__init__.py
similarity index 100%
rename from __init__.py
rename to src/__init__.py
diff --git a/cache.py b/src/cache.py
similarity index 100%
rename from cache.py
rename to src/cache.py
diff --git a/src/config.py b/src/config.py
new file mode 100644
index 0000000..fb11114
--- /dev/null
+++ b/src/config.py
@@ -0,0 +1,71 @@
+import os
+import yaml
+
+WIKMD_CONFIG_FILE = "../config.yaml"
+
+def config_list(yaml_config, config_item_name):
+    """
+    Function that gets a config item of type list.
+    Priority is in the following order either from environment variables or yaml file or default value.
+    """
+    default_value = ["image/gif", "image/jpeg", "image/png", "image/svg+xml", "image/webp"]
+    if os.getenv(config_item_name.upper()):
+        # Env Var in the form `EXAMPLE="a, b, c, d"` or `EXAMPLE="a,b,c,d"`
+        return [ext.strip() for ext in os.getenv(config_item_name.upper()).split(",")]
+    elif yaml_config[config_item_name.lower()]:
+        return yaml_config[config_item_name.lower()]
+    else:
+        return default_value
+
+
+class WikmdConfig:
+    """
+    Class that stores the configuration of wikmd.
+    """
+    def __init__(self):
+        """
+        Function that gets the configuration parameters from .yaml file, os environment variables or default values.
+        Each configuration parameter is stored into a class attribute.
+        Env. vars take precedence.
+        """
+        __location__ = os.path.realpath(
+            os.path.join(os.getcwd(), os.path.dirname(__file__)))
+
+        # .yaml config file
+        with open(os.path.join(__location__, WIKMD_CONFIG_FILE)) as f:
+            yaml_config = yaml.safe_load(f)
+
+        # Load config parameters from env. vars, yaml or default values (the firsts take precedence)
+        self.wikmd_host = yaml_config.get("wikmd_host")
+        self.wikmd_port =  yaml_config.get("wikmd_port")
+        self.wikmd_logging = yaml_config.get("wikmd_logging")
+        self.wikmd_logging_file = yaml_config.get("wikmd_logging_file")
+
+        self.git_user = yaml_config.get("git_user")
+        self.git_email = yaml_config.get("git_email")
+
+        self.main_branch_name = yaml_config.get("main_branch_name")
+        self.sync_with_remote = yaml_config.get("sync_with_remote")
+        self.remote_url = yaml_config.get("remote_url")
+
+        self.wiki_directory = yaml_config.get("wiki_directory")
+        self.homepage = yaml_config.get("homepage")
+        self.homepage_title = yaml_config.get("homepage_title")
+        self.images_route = yaml_config.get("images_route")
+
+        self.hide_folder_in_wiki = yaml_config.get("hide_folder_in_wiki")
+
+        self.plugins = yaml_config.get("plugins")
+
+        self.protect_edit_by_password = yaml_config.get("protect_edit_by_password")
+        self.password_in_sha_256 = yaml_config.get("password_in_sha_256")
+
+        self.local_mode = yaml_config.get("local_mode")
+
+        self.image_allowed_mime = config_list(yaml_config, "image_allowed_mime")
+        self.optimize_images = yaml_config.get("optimize_images", )
+
+        self.cache_dir = yaml_config.get("cache_dir")
+        self.search_dir = yaml_config.get("search_dir")
+
+        self.secret_key = yaml_config.get("secret_key")
diff --git a/git_manager.py b/src/git_manager.py
similarity index 99%
rename from git_manager.py
rename to src/git_manager.py
index 2590e27..7954d62 100644
--- a/git_manager.py
+++ b/src/git_manager.py
@@ -8,13 +8,10 @@
 from config import WikmdConfig
 from utils import move_all_files
 
-
 TEMP_DIR = "temp"
 
-
 cfg = WikmdConfig()
 
-
 def is_git_repo(path: str) -> bool:
     """
     Function that determines if the given path is a git repo.
diff --git a/image_manager.py b/src/image_manager.py
similarity index 100%
rename from image_manager.py
rename to src/image_manager.py
diff --git a/knowledge_graph.py b/src/knowledge_graph.py
similarity index 99%
rename from knowledge_graph.py
rename to src/knowledge_graph.py
index af24e1d..5613884 100644
--- a/knowledge_graph.py
+++ b/src/knowledge_graph.py
@@ -6,7 +6,6 @@
 
 cfg = WikmdConfig()
 
-
 def extend_ids(links):
     for link in links:
         for l in link["links"]:
diff --git a/plugins/__init__.py b/src/plugins/__init__.py
similarity index 100%
rename from plugins/__init__.py
rename to src/plugins/__init__.py
diff --git a/plugins/alerts/__init__.py b/src/plugins/alerts/__init__.py
similarity index 100%
rename from plugins/alerts/__init__.py
rename to src/plugins/alerts/__init__.py
diff --git a/plugins/alerts/alerts.py b/src/plugins/alerts/alerts.py
similarity index 100%
rename from plugins/alerts/alerts.py
rename to src/plugins/alerts/alerts.py
diff --git a/plugins/draw/__init__.py b/src/plugins/draw/__init__.py
similarity index 100%
rename from plugins/draw/__init__.py
rename to src/plugins/draw/__init__.py
diff --git a/plugins/draw/default_draw b/src/plugins/draw/default_draw
similarity index 100%
rename from plugins/draw/default_draw
rename to src/plugins/draw/default_draw
diff --git a/plugins/draw/draw.py b/src/plugins/draw/draw.py
similarity index 100%
rename from plugins/draw/draw.py
rename to src/plugins/draw/draw.py
diff --git a/plugins/draw/drawings/.gitignore b/src/plugins/draw/drawings/.gitignore
similarity index 100%
rename from plugins/draw/drawings/.gitignore
rename to src/plugins/draw/drawings/.gitignore
diff --git a/plugins/embed-pages/__init__.py b/src/plugins/embed-pages/__init__.py
similarity index 100%
rename from plugins/embed-pages/__init__.py
rename to src/plugins/embed-pages/__init__.py
diff --git a/plugins/embed-pages/embed-pages.py b/src/plugins/embed-pages/embed-pages.py
similarity index 100%
rename from plugins/embed-pages/embed-pages.py
rename to src/plugins/embed-pages/embed-pages.py
diff --git a/plugins/load_plugins.py b/src/plugins/load_plugins.py
similarity index 100%
rename from plugins/load_plugins.py
rename to src/plugins/load_plugins.py
diff --git a/plugins/mermaid/__init__.py b/src/plugins/mermaid/__init__.py
similarity index 100%
rename from plugins/mermaid/__init__.py
rename to src/plugins/mermaid/__init__.py
diff --git a/plugins/mermaid/mermaid.py b/src/plugins/mermaid/mermaid.py
similarity index 100%
rename from plugins/mermaid/mermaid.py
rename to src/plugins/mermaid/mermaid.py
diff --git a/search.py b/src/search.py
similarity index 100%
rename from search.py
rename to src/search.py
diff --git a/utils.py b/src/utils.py
similarity index 100%
rename from utils.py
rename to src/utils.py
diff --git a/web_dependencies.py b/src/web_dependencies.py
similarity index 100%
rename from web_dependencies.py
rename to src/web_dependencies.py
diff --git a/wiki.py b/src/wiki.py
similarity index 99%
rename from wiki.py
rename to src/wiki.py
index b5435c3..a5be1dc 100644
--- a/wiki.py
+++ b/src/wiki.py
@@ -8,12 +8,11 @@
 import knowledge_graph
 import secrets
 
-from flask import Flask, render_template, request, redirect, url_for, make_response, send_file, \
-    send_from_directory, flash
-
+from flask import Flask, render_template, request, redirect, url_for, make_response, send_file, send_from_directory, flash
 from werkzeug.utils import safe_join, secure_filename
 from threading import Thread
 from hashlib import sha256
+
 from cache import Cache
 from image_manager import ImageManager
 from config import WikmdConfig
@@ -21,9 +20,9 @@
 from search import Search, Watchdog
 from web_dependencies import get_web_deps
 from plugins.load_plugins import PluginLoader
-
 from utils import pathify
 
+
 SESSIONS = []
 
 cfg = WikmdConfig()
@@ -34,7 +33,8 @@
 HOMEPAGE_PATH = pathify(cfg.wiki_directory, cfg.homepage)
 HIDDEN_PATHS = tuple([UPLOAD_FOLDER_PATH, GIT_FOLDER_PATH, HOMEPAGE_PATH] + HIDDEN_FOLDER_PATH_LIST)
 
-app = Flask(__name__)
+app = Flask(__name__, template_folder="../templates", static_folder="../static")
+
 app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER_PATH
 app.config['SECRET_KEY'] = cfg.secret_key