diff --git a/docs/.gitignore b/docs/.gitignore
deleted file mode 100644
index 75bda11e..00000000
--- a/docs/.gitignore
+++ /dev/null
@@ -1,5 +0,0 @@
-/03_api/*
-jupyter_execute
-_toc.yml
-.jupyter_cache
-conf.py
diff --git a/docs/01_tutorials/00_example.rst b/docs/01_tutorials/00_example.rst
deleted file mode 100644
index 88ddbae1..00000000
--- a/docs/01_tutorials/00_example.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-Example
-=======
-This is a placeholder for the example.
-
-Citation example
-----------------
-It contains an example of citation :cite:`TURING.1950`.
-
-.. bibliography:: /refs.bib
-    :style: unsrtalpha
-    :filter: docname in docnames
diff --git a/docs/01_tutorials/index.rst b/docs/01_tutorials/index.rst
deleted file mode 100644
index f08b66f9..00000000
--- a/docs/01_tutorials/index.rst
+++ /dev/null
@@ -1,2 +0,0 @@
-Tutorials
-=========
\ No newline at end of file
diff --git a/docs/02_notebooks/00_intro.md b/docs/02_notebooks/00_intro.md
deleted file mode 100644
index 07879ddf..00000000
--- a/docs/02_notebooks/00_intro.md
+++ /dev/null
@@ -1,4 +0,0 @@
-# Notebook Tutorials
-
-Here is a collection of executable tutorials for serena. 
-You can run them directly in colab, or download them and run them locally.
diff --git a/docs/02_notebooks/01_library_example.ipynb b/docs/02_notebooks/01_library_example.ipynb
deleted file mode 100644
index 6516e859..00000000
--- a/docs/02_notebooks/01_library_example.ipynb
+++ /dev/null
@@ -1,128 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# The role of notebooks\n",
-    "\n",
-    "Notebooks are great for illustrations and examples that at the same time serve as integration tests.\n",
-    "In this library template, notebooks will be executed with pytest (thus on every\n",
-    "commit in your CI/CD pipeline). The results of the executions will be saved to the docs directory and converted to\n",
-    "static websites through nbconvert. The static websites are then added to the documentation under the\n",
-    "_Guides and Tutorials_ section. These websites will be deployed to Github pages on push to develop."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Before running the notebook\n",
-    "\n",
-    "Install the library and its dependencies with, if you haven't done so already\n",
-    "```\n",
-    "poetry install\n",
-    "```\n",
-    "from the root directory. You can also execute this command directly in the notebook but will need to reload the\n",
-    "kernel afterwards"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# Here an illustration of your library\n",
-    "from serena.sample_package.sample_module import hello_stranger\n",
-    "\n",
-    "hello_stranger()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "pycharm": {
-     "name": "#%% md\n"
-    }
-   },
-   "source": [
-    "## Interactive Documentation\n",
-    "\n",
-    "Note that since notebooks are rendered to html+javascript, you can embed interactive components like maps, videos and\n",
-    "widgets into your documentation, as long as the interaction does not require re-execution of cells.\n",
-    "Below an example of an interactive map created with plotly {cite}`PlotlyMaps`."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# slightly adjusted example from https://plotly.com/python/mapbox-layers/\n",
-    "import pandas as pd\n",
-    "import plotly.express as px\n",
-    "\n",
-    "us_cities = pd.read_csv(\n",
-    "    \"https://raw.githubusercontent.com/plotly/datasets/master/us-cities-top-1k.csv\",\n",
-    ")\n",
-    "\n",
-    "fig = px.scatter_mapbox(\n",
-    "    us_cities,\n",
-    "    lat=\"lat\",\n",
-    "    lon=\"lon\",\n",
-    "    hover_name=\"City\",\n",
-    "    hover_data=[\"State\", \"Population\"],\n",
-    "    color_discrete_sequence=[\"fuchsia\"],\n",
-    "    zoom=3,\n",
-    "    height=300,\n",
-    ")\n",
-    "\n",
-    "fig.update_layout(mapbox_style=\"open-street-map\", margin={\"r\": 0, \"t\": 0, \"l\": 0, \"b\": 0})\n",
-    "fig.show()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "source": [
-    "```{bibliography}\n",
-    ":style: unsrtalpha\n",
-    ":filter: docname in docnames\n",
-    "```"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
diff --git a/docs/04_contributing/04_contributing.rst b/docs/04_contributing/04_contributing.rst
deleted file mode 100644
index c43ed729..00000000
--- a/docs/04_contributing/04_contributing.rst
+++ /dev/null
@@ -1,91 +0,0 @@
-Contributing to serena
-=============================================
-
-
-Install Develop Version
------------------------
-
-serena is built and managed by `poetry <https://python-poetry.org/>`_. For example,
-to install all relevant requirements in editable mode you can simply call
-
-.. code-block:: bash
-
-  $ poetry install --with dev
-
-
-PEP8 Code Style Check and Formatting
-----------------------------------------
-
-Please set up pre-commit by running
-
-.. code-block:: bash
-
-    $ pre-commit install
-
-in the main directory. This should make sure that your contribution is properly
-formatted before every commit.
-
-The code is inspected and formatted by `black` and `ruff`. They are executed as
-pre-commit hooks. In addition, `poe the poet` tasks are configured.
-Simply run `poe` to see the available tasks.
-E.g, to format and check the linting manually you can run:
-
-.. code-block:: bash
-
-    $ poe format
-    $ poe lint
-
-
-Type Check
-----------
-
-We use `mypy <https://github.com/python/mypy/>`_ to check the type annotations. To check, in the main directory, run:
-
-.. code-block:: bash
-
-    $ poe type-check
-
-
-Test Locally
-------------
-
-This command will run automatic tests in the main directory
-
-.. code-block:: bash
-
-    $ poe test
-
-
-Documentation
--------------
-
-Documentations are written under the ``docs/`` directory as ReStructuredText (``.rst``) files. ``index.rst`` is the main page. A Tutorial on ReStructuredText can be found `here <https://pythonhosted.org/an_example_pypi_project/sphinx.html>`_.
-
-API References are automatically generated by `Sphinx <http://www.sphinx-doc.org/en/stable/>`_ according to the outlines under ``docs/api/`` and should be modified when any code changes.
-
-To compile documentation into webpage, run
-
-.. code-block:: bash
-
-    $ poe doc-build
-
-The generated webpage is in ``docs/_build`` and can be viewed with browser (http://0.0.0.0:8000/).
-
-
-Documentation Generation Test
------------------------------
-
-We have the following three documentation tests:
-
-1. pydocstyle (as part of ruff): test all docstrings;
-
-2. doc8 (as part of ruff): test ReStructuredText format;
-
-3. sphinx spelling and test: test if there is any error/warning when generating front-end html documentation.
-
-To check, in the main directory, run:
-
-.. code-block:: bash
-
-    $ poe lint
-    $ poe doc-build
diff --git a/docs/_config.yml b/docs/_config.yml
deleted file mode 100644
index e7701f5b..00000000
--- a/docs/_config.yml
+++ /dev/null
@@ -1,147 +0,0 @@
-# Book settings
-# Learn more at https://jupyterbook.org/customize/config.html
-
-#######################################################################################
-# A default configuration that will be loaded for all jupyter books
-# Users are expected to override these values in their own `_config.yml` file.
-# This is also the "master list" of all allowed keys and values.
-
-#######################################################################################
-# Book settings
-title                       : serena Documentation  # The title of the book. Will be placed in the left navbar.
-author                      : serena contributors  # The author of the book
-copyright                   : ""  # Copyright year to be placed in the footer
-logo                        : "" # A path to the book logo
-# Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb")
-exclude_patterns            : ['**.ipynb_checkpoints', '.DS_Store', 'Thumbs.db', '_build', 'jupyter_execute', '.jupyter_cache', '.pytest_cache', 'docs/autogen_rst.py', 'docs/create_toc.py']
-# Auto-exclude files not in the toc
-only_build_toc_files        : false
-
-#######################################################################################
-# Execution settings
-execute:
-  execute_notebooks         : cache  # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
-  cache                     : ""    # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
-  exclude_patterns          : []    # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
-  timeout                   : -1    # The maximum time (in seconds) each notebook cell is allowed to run.
-  run_in_temp               : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),
-                                    # otherwise the notebook's parent directory will be the cwd.
-  allow_errors              : false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run.
-  stderr_output             : show  # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe'
-
-#######################################################################################
-# Parse and render settings
-parse:
-  myst_enable_extensions: # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html
-    - amsmath
-    - colon_fence
-    # - deflist
-    - dollarmath
-    # - html_admonition
-    # - html_image
-    - linkify
-    # - replacements
-    # - smartquotes
-    - substitution
-    - tasklist
-  myst_url_schemes: [ mailto, http, https ] # URI schemes that will be recognised as external URLs in Markdown links
-  myst_dmath_double_inline: true  # Allow display math ($$) within an inline context
-
-#######################################################################################
-# HTML-specific settings
-html:
-  favicon                   : ""  # A path to a favicon image
-  use_edit_page_button      : false  # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in
-  use_repository_button     : false  # Whether to add a link to your repository button
-  use_issues_button         : false  # Whether to add an "open an issue" button
-  use_multitoc_numbering    : true   # Continuous numbering across parts/chapters
-  extra_footer              : ""
-  google_analytics_id       : ""  # A GA id that can be used to track book views.
-  home_page_in_navbar       : true  # Whether to include your home page in the left Navigation Bar
-  baseurl                   : "https://github.com/oraios/serena"
-  analytics:
-
-  comments:
-    hypothesis              : false
-    utterances              : false
-  announcement              : "" # A banner announcement at the top of the site.
-
-#######################################################################################
-# LaTeX-specific settings
-latex:
-  latex_engine              : pdflatex  # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex'
-  use_jupyterbook_latex     : true # use sphinx-jupyterbook-latex for pdf builds as default
-  targetname                : book.tex
-# Add a bibtex file so that we can create citations
-bibtex_bibfiles:
-  - refs.bib
-
-#######################################################################################
-# Launch button settings
-launch_buttons:
-  notebook_interface        : classic  # The interface interactive links will activate ["classic", "jupyterlab"]
-  binderhub_url             : ""  # The URL of the BinderHub (e.g., https://mybinder.org)
-  jupyterhub_url            : ""  # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu)
-  thebe                     : false  # Add a thebe button to pages (requires the repository to run on Binder)
-  colab_url                 : "https://colab.research.google.com"
-
-repository:
-  url                       : https://github.com/oraios/serena  # The URL to your book's repository
-  path_to_book              : docs  # A path to your book's folder, relative to the repository root.
-  branch                    : main  # Which branch of the repository should be used when creating links
-
-#######################################################################################
-# Advanced and power-user settings
-sphinx:
-  extra_extensions          :
-    - sphinx.ext.autodoc
-    - sphinx.ext.viewcode
-    - sphinx_toolbox.more_autodoc.sourcelink
-    - sphinxcontrib.spelling
-  local_extensions          :   # A list of local extensions to load by sphinx specified by "name: path" items
-  recursive_update          : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update (false)
-  config                    :   # key-value pairs to directly over-ride the Sphinx configuration
-    autodoc_typehints_format: "short"
-    autodoc_member_order: "bysource"
-    autoclass_content: "both"
-    autodoc_default_options:
-      show-inheritance: True
-    suppress_warnings: ["mystnb.unknown_mime_type"]  # needed for plotly rendering
-    autodoc_show_sourcelink: True
-    add_module_names: False
-    github_username: oraios
-    github_repository: https://github.com/oraios/serena
-    python_use_unqualified_type_names: True
-    nb_mime_priority_overrides: [
-      [ 'html', 'application/vnd.jupyter.widget-view+json', 10 ],
-      [ 'html', 'application/javascript', 20 ],
-      [ 'html', 'text/html', 30 ],
-      [ 'html', 'text/latex', 40 ],
-      [ 'html', 'image/svg+xml', 50 ],
-      [ 'html', 'image/png', 60 ],
-      [ 'html', 'image/jpeg', 70 ],
-      [ 'html', 'text/markdown', 80 ],
-      [ 'html', 'text/plain', 90 ],
-      [ 'spelling', 'application/vnd.jupyter.widget-view+json', 10 ],
-      [ 'spelling', 'application/javascript', 20 ],
-      [ 'spelling', 'text/html', 30 ],
-      [ 'spelling', 'text/latex', 40 ],
-      [ 'spelling', 'image/svg+xml', 50 ],
-      [ 'spelling', 'image/png', 60 ],
-      [ 'spelling', 'image/jpeg', 70 ],
-      [ 'spelling', 'text/markdown', 80 ],
-      [ 'spelling', 'text/plain', 90 ],
-    ]
-    mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
-    mathjax3_config:
-      loader: { load: [ '[tex]/configmacros' ] }
-      tex:
-        packages: { '[+]': [ 'configmacros' ] }
-        macros:
-          vect: ["{\\mathbf{\\boldsymbol{#1}} }", 1]
-          E: "{\\mathbb{E}}"
-          P: "{\\mathbb{P}}"
-          R: "{\\mathbb{R}}"
-          abs: ["{\\left| #1 \\right|}", 1]
-          simpl: ["{\\Delta^{#1} }", 1]
-          amax: "{\\text{argmax}}"
\ No newline at end of file
diff --git a/docs/_static/css/style.css b/docs/_static/css/style.css
deleted file mode 100644
index e929c466..00000000
--- a/docs/_static/css/style.css
+++ /dev/null
@@ -1,138 +0,0 @@
-body {
-    font-family: "Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;
-}
-
-/* Default header fonts are ugly */
-h1, h2, .rst-content .toctree-wrapper p.caption, h3, h4, h5, h6, legend, p.caption {
-    font-family: "Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;
-}
-
-/* Use white for docs background */
-.wy-side-nav-search {
-    background-color: #fff;
-}
-
-.wy-nav-content {
-    max-width: 1200px !important;
-}
-
-.wy-nav-content-wrap, .wy-menu li.current > a  {
-    background-color: #fff;
-}
-
-.wy-side-nav-search>a img.logo {
-    width: 80%;
-    margin-top: 10px;
-}
-
-@media screen and (min-width: 1400px) {
-    .wy-nav-content-wrap {
-        background-color: #fff;
-    }
-
-    .wy-nav-content {
-        background-color: #fff;
-    }
-}
-
-/* Fixes for mobile */
-.wy-nav-top {
-    background-color: #fff;
-    background-repeat: no-repeat;
-    background-position: center;
-    padding: 0;
-    margin: 0.4045em 0.809em;
-    color: #333;
-}
-
-.wy-nav-top > a {
-    display: none;
-}
-
-@media screen and (max-width: 768px) {
-    .wy-side-nav-search>a img.logo {
-        height: 60px;
-    }
-}
-
-/* This is needed to ensure that logo above search scales properly */
-.wy-side-nav-search a {
-    display: block;
-}
-
-/* This ensures that multiple constructors will remain in separate lines. */
-.rst-content dl:not(.docutils) dt {
-    display: table;
-}
-
-/* Use our red for literals (it's very similar to the original color) */
-.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal {
-    color: #4692BC;
-}
-
-.rst-content tt.xref, a .rst-content tt, .rst-content tt.xref,
-.rst-content code.xref, a .rst-content tt, a .rst-content code {
-    color: #404040;
-}
-
-/* Change link colors (except for the menu) */
-
-a {
-    color: #4692BC;
-}
-
-a:hover {
-    color: #4692BC;
-}
-
-
-a:visited {
-    color: #4692BC;
-}
-
-.wy-menu a {
-    color: #b3b3b3;
-}
-
-.wy-menu a:hover {
-    color: #b3b3b3;
-}
-
-/* Default footer text is quite big */
-footer {
-    font-size: 80%;
-}
-
-footer .rst-footer-buttons {
-    font-size: 125%; /* revert footer settings - 1/80% = 125% */
-}
-
-footer p {
-    font-size: 100%;
-}
-
-.ethical-rtd {
-    display: none;
-}
-
-.ethical-fixedfooter {
-    display: none;
-}
-
-.ethical-content {
-    display: none;
-}
-
-/* For hidden headers that appear in TOC tree */
-/* see http://stackoverflow.com/a/32363545/3343043 */
-.rst-content .hidden-section {
-    display: none;
-}
-
-nav .hidden-section {
-    display: inherit;
-}
-
-.wy-side-nav-search>div.version {
-    color: #000;
-}
diff --git a/docs/_static/js/require.min.js b/docs/_static/js/require.min.js
deleted file mode 100644
index a4203f0d..00000000
--- a/docs/_static/js/require.min.js
+++ /dev/null
@@ -1,5 +0,0 @@
-/** vim: et:ts=4:sw=4:sts=4
- * @license RequireJS 2.3.6 Copyright jQuery Foundation and other contributors.
- * Released under MIT license, https://github.com/requirejs/requirejs/blob/master/LICENSE
- */
-var requirejs,require,define;!function(global,setTimeout){var req,s,head,baseElement,dataMain,src,interactiveScript,currentlyAddingScript,mainScript,subPath,version="2.3.6",commentRegExp=/\/\*[\s\S]*?\*\/|([^:"'=]|^)\/\/.*$/gm,cjsRequireRegExp=/[^.]\s*require\s*\(\s*["']([^'"\s]+)["']\s*\)/g,jsSuffixRegExp=/\.js$/,currDirRegExp=/^\.\//,op=Object.prototype,ostring=op.toString,hasOwn=op.hasOwnProperty,isBrowser=!("undefined"==typeof window||"undefined"==typeof navigator||!window.document),isWebWorker=!isBrowser&&"undefined"!=typeof importScripts,readyRegExp=isBrowser&&"PLAYSTATION 3"===navigator.platform?/^complete$/:/^(complete|loaded)$/,defContextName="_",isOpera="undefined"!=typeof opera&&"[object Opera]"===opera.toString(),contexts={},cfg={},globalDefQueue=[],useInteractive=!1;function commentReplace(e,t){return t||""}function isFunction(e){return"[object Function]"===ostring.call(e)}function isArray(e){return"[object Array]"===ostring.call(e)}function each(e,t){var 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diff --git a/docs/autogen_rst.py b/docs/autogen_rst.py
deleted file mode 100644
index 8c6d8a79..00000000
--- a/docs/autogen_rst.py
+++ /dev/null
@@ -1,141 +0,0 @@
-import logging
-import os
-import shutil
-from pathlib import Path
-
-log = logging.getLogger(os.path.basename(__file__))
-
-
-def module_template(module_qualname: str):
-    module_name = module_qualname.split(".")[-1]
-    title = module_name.replace("_", r"\_")
-    return f"""{title}
-{"=" * len(title)}
-
-.. automodule:: {module_qualname}
-   :members:
-   :undoc-members:
-"""
-
-
-def index_template(package_name: str, doc_references: list[str] | None = None, text_prefix=""):
-    doc_references = doc_references or ""
-    if doc_references:
-        doc_references = "\n" + "\n".join(f"* :doc:`{ref}`" for ref in doc_references) + "\n"
-
-    dirname = package_name.split(".")[-1]
-    title = dirname.replace("_", r"\_")
-    if title == "serena":
-        title = "serena API Reference"
-    return f"{title}\n{'=' * len(title)}" + text_prefix + doc_references
-
-
-def write_to_file(content: str, path: str):
-    os.makedirs(os.path.dirname(path), exist_ok=True)
-    with open(path, "w") as f:
-        f.write(content)
-    os.chmod(path, 0o666)
-
-
-_SUBTITLE = (
-    "\n Here is the autogenerated documentation of the serena API. \n \n "
-    "The Table of Contents to the left has the same structure as the "
-    "repository's package code. The links at each page point to the submodules and subpackages. \n\n "
-    "Enjoy scrolling through! \n"
-)
-
-
-def make_rst(src_root, rst_root, clean=False, overwrite=False, package_prefix=""):
-    """Creates/updates documentation in form of rst files for modules and packages.
-
-    Does not delete any existing rst files. Thus, rst files for packages or modules that have been removed or renamed
-    should be deleted by hand.
-
-    This method should be executed from the project's top-level directory
-
-    :param src_root: path to library base directory, typically "src/<library_name>"
-    :param clean: whether to completely clean the target directory beforehand, removing any existing .rst files
-    :param overwrite: whether to overwrite existing rst files. This should be used with caution as it will delete
-        all manual changes to documentation files
-    :package_prefix: a prefix to prepend to each module (for the case where the src_root is not the base package),
-        which, if not empty, should end with a "."
-    :return:
-    """
-    rst_root = os.path.abspath(rst_root)
-
-    if clean and os.path.isdir(rst_root):
-        shutil.rmtree(rst_root)
-
-    base_package_name = package_prefix + os.path.basename(src_root)
-
-    # TODO: reduce duplication with same logic for subpackages below
-    files_in_dir = os.listdir(src_root)
-    module_names = [f[:-3] for f in files_in_dir if f.endswith(".py") and not f.startswith("_")]
-    subdir_refs = [f"{f}/index" for f in files_in_dir if os.path.isdir(os.path.join(src_root, f)) and not f.startswith("_")]
-    package_index_rst_path = os.path.join(
-        rst_root,
-        "index.rst",
-    )
-    log.info(f"Writing {package_index_rst_path}")
-    write_to_file(
-        index_template(
-            base_package_name,
-            doc_references=module_names + subdir_refs,
-            text_prefix=_SUBTITLE,
-        ),
-        package_index_rst_path,
-    )
-
-    for root, dirnames, filenames in os.walk(src_root):
-        if os.path.basename(root).startswith("_"):
-            continue
-        base_package_relpath = os.path.relpath(root, start=src_root)
-        base_package_qualname = package_prefix + os.path.relpath(
-            root,
-            start=os.path.dirname(src_root),
-        ).replace(os.path.sep, ".")
-
-        for dirname in dirnames:
-            if dirname.startswith("_"):
-                log.debug(f"Skipping {dirname}")
-                continue
-            files_in_dir = os.listdir(os.path.join(root, dirname))
-            module_names = [f[:-3] for f in files_in_dir if f.endswith(".py") and not f.startswith("_")]
-            subdir_refs = [f"{f}/index" for f in files_in_dir if os.path.isdir(os.path.join(root, dirname, f)) and not f.startswith("_")]
-            if not module_names:
-                log.debug(f"Skipping {dirname} as it does not contain any .py files")
-                continue
-            package_qualname = f"{base_package_qualname}.{dirname}"
-            package_index_rst_path = os.path.join(
-                rst_root,
-                base_package_relpath,
-                dirname,
-                "index.rst",
-            )
-            log.info(f"Writing {package_index_rst_path}")
-            write_to_file(
-                index_template(package_qualname, doc_references=module_names + subdir_refs),
-                package_index_rst_path,
-            )
-
-        for filename in filenames:
-            base_name, ext = os.path.splitext(filename)
-            if ext == ".py" and not filename.startswith("_"):
-                module_qualname = f"{base_package_qualname}.{filename[:-3]}"
-
-                module_rst_path = os.path.join(rst_root, base_package_relpath, f"{base_name}.rst")
-                if os.path.exists(module_rst_path) and not overwrite:
-                    log.debug(f"{module_rst_path} already exists, skipping it")
-
-                log.info(f"Writing module documentation to {module_rst_path}")
-                write_to_file(module_template(module_qualname), module_rst_path)
-
-
-if __name__ == "__main__":
-    logging.basicConfig(level=logging.INFO)
-    docs_root = Path(__file__).parent
-    make_rst(
-        docs_root / ".." / "src" / "serena",
-        docs_root / "03_api",
-        clean=True,
-    )
diff --git a/docs/bibtex.json b/docs/bibtex.json
deleted file mode 100644
index 175e65ec..00000000
--- a/docs/bibtex.json
+++ /dev/null
@@ -1,10 +0,0 @@
-{
-    "cited": {
-        "01_tutorials/00_example": [
-            "TURING.1950"
-        ],
-        "02_notebooks/00_example": [
-            "PlotlyMaps"
-        ]
-    }
-}
\ No newline at end of file
diff --git a/docs/create_toc.py b/docs/create_toc.py
deleted file mode 100644
index 3e1779cd..00000000
--- a/docs/create_toc.py
+++ /dev/null
@@ -1,8 +0,0 @@
-import os
-from pathlib import Path
-
-# This script provides a platform-independent way of making the jupyter-book call (used in pyproject.toml)
-toc_file = Path(__file__).parent / "_toc.yml"
-cmd = f"jupyter-book toc from-project docs -e .rst -e .md -e .ipynb  >{toc_file}"
-print(cmd)
-os.system(cmd)
diff --git a/docs/index.rst b/docs/index.rst
deleted file mode 100644
index 2cdc89b8..00000000
--- a/docs/index.rst
+++ /dev/null
@@ -1,15 +0,0 @@
-Welcome to serena!
-=========================================
-
-Welcome to the serena library.
-See the project's repository_  for more information.
-
-.. _repository: https://github.com/oraios/serena
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/docs/nbstripout.py b/docs/nbstripout.py
deleted file mode 100644
index 1302a35f..00000000
--- a/docs/nbstripout.py
+++ /dev/null
@@ -1,11 +0,0 @@
-"""Implements a platform-independent way of calling nbstripout (used in pyproject.toml)."""
-
-import glob
-import os
-from pathlib import Path
-
-if __name__ == "__main__":
-    docs_dir = Path(__file__).parent
-    for path in glob.glob(str(docs_dir / "02_notebooks" / "*.ipynb")):
-        cmd = f"nbstripout {path}"
-        os.system(cmd)
diff --git a/docs/refs.bib b/docs/refs.bib
deleted file mode 100644
index 98c79a29..00000000
--- a/docs/refs.bib
+++ /dev/null
@@ -1,21 +0,0 @@
-@article{TURING.1950,
- author = {TURING, A. M.},
- year = {1950},
- title = {I.---COMPUTING MACHINERY AND INTELLIGENCE},
- pages = {433--460},
- volume = {LIX},
- number = {236},
- issn = {0026-4423},
- journal = {Mind},
- doi = {10.1093/mind/LIX.236.433},
- file = {ICOMPUTING MACHINERY AND INTELLIGENCE:Attachments/ICOMPUTING MACHINERY AND INTELLIGENCE.pdf:application/pdf}
-}
-
-
-@misc{PlotlyMaps,
- abstract = {Plotly's},
- year = {2/16/2024},
- title = {Maps},
- url = {https://plotly.com/python/maps/},
- urldate = {2/28/2024}
-}
\ No newline at end of file
diff --git a/docs/spelling_wordlist.txt b/docs/spelling_wordlist.txt
deleted file mode 100644
index c634d4e1..00000000
--- a/docs/spelling_wordlist.txt
+++ /dev/null
@@ -1,21 +0,0 @@
-serena
-serena
-Oraios AI
-oraios
-
-appliedAI
-autogenerated
-colab
-docstring
-docstrings
-Github
-html
-init
-javascript
-pre
-pycharm
-pydocstyle
-submodules
-subpackages
-utils
-webpage
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 5dd97316..09fa7a9b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,29 +41,15 @@ text = "MIT"
 [project.optional-dependencies]
 dev = [
   "black[jupyter]>=23.7.0",
-  "docutils>=0.20.1",
   "jinja2",
-  "jupyter>=1.0.0",
   # In version 1.0.4 we get a NoneType error related to some config conversion (yml_analytics is None and should be a list)
-  "jupyter-book==1.0.0",
   "mypy>=1.4.1",
-  "nbqa>=1.7.1",
-  "nbstripout>=0.6.1",
   "poethepoet>=0.20.0",
   "pre-commit>=3.3.3",
   "pytest>=8.0.2",
   "pytest-cov",
   "ruff>=0.0.285",
-  "sphinx>=7",
-  "sphinx-book-theme>=1.0.1",
-  "sphinx-comments>=0.0.3",
-  "sphinx-copybutton>=0.5.2",
-  "sphinx-jupyterbook-latex>=1.0.0",
   "toml-sort>=0.24.2",
-  "sphinx-togglebutton>=0.3.2",
-  "sphinx-toolbox>=3.5.0",
-  "sphinxcontrib-bibtex",
-  "sphinxcontrib-spelling>=8.0.0",
   "types-pyyaml>=6.0.12.20241230",
 ]
 agno = [
@@ -109,10 +95,6 @@ warn_unused_configs = true
 warn_unused_ignores = true
 exclude = "^build/|^docs/"
 
-[tool.nbqa.exclude]
-ruff = "\\.jupyter_cache|jupyter_execute"
-mypy = "\\.jupyter_cache|jupyter_execute"
-
 [tool.poe.env]
 PYDEVD_DISABLE_FILE_VALIDATION = "1"
 
@@ -120,19 +102,15 @@ PYDEVD_DISABLE_FILE_VALIDATION = "1"
 test = "pytest test --cov=serena --cov-report=xml --cov-report=term-missing --durations=0 -v --color=yes"
 _black_check = "black --check --exclude src/multilspy/ src scripts test"
 _ruff_check = "ruff check --exclude .venv/ --exclude src/multilspy/ src scripts test"
-_ruff_check_nb = "nbqa ruff check docs"
 _black_format = "black --exclude .venv/|src/multilspy/ src scripts test"
 _ruff_format = "ruff check --exclude src/multilspy/ --fix src scripts test"
-_ruff_format_nb = "nbqa ruff --fix docs"
 lint = [
   "_black_check",
   "_ruff_check",
-  #"_ruff_check_nb"
 ]
 clean-nbs = "python docs/nbstripout.py"
 format = [
   "_ruff_format",
-  "_ruff_format_nb",
   "_black_format"
 ]
 _autogen_rst = "python docs/autogen_rst.py"
@@ -152,10 +130,8 @@ doc-build = [
   "_sphinx_build"
 ]
 _mypy = "mypy src/serena"
-_mypy_nb = "nbqa mypy docs"
 type-check = [
   "_mypy",
-  "_mypy_nb"
 ]
 
 [tool.ruff]