diff --git a/docs/Makefile b/docs/Makefile
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -16,6 +16,7 @@
 APIDOC_EXCLUDES = */tests */tests/* */*/tests/* */*/*/tests/*
 APIDOC_EXCLUDES += */migrations */migrations/* */*/migrations/* */*/*/migrations/*
 APIDOC_EXCLUDES += */wsgi.py */*/wsgi.py */*/*/wsgi.py */*/*/wsgi.py
+APIDOC_EXCLUDES += deposit/settings/* web/settings/* dataset/*
 APIDOC_SWH_EXCLUDES = $(patsubst %,$(SWHPKGDIR)/%,$(APIDOC_EXCLUDES))
 
 html: sphinx/html
diff --git a/docs/index.rst b/docs/index.rst
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -59,27 +59,15 @@
 :ref:`swh.loader-core <swh-loader-core>`
     low-level loading utilities and helpers used by all other loaders
 
-:ref:`swh.loader-debian <swh-loader-debian>`
-    loader for `Debian <https://www.debian.org/>`_ source packages
-
-:ref:`swh.loader-dir <swh-loader-dir>`
-    loader for source directories (e.g., expanded tarballs)
-
 :ref:`swh.loader-git <swh-loader-git>`
     loader for `Git <https://git-scm.com/>`_ repositories
 
 :ref:`swh.loader-mercurial <swh-loader-mercurial>`
     loader for `Mercurial <https://www.mercurial-scm.org/>`_ repositories
 
-:ref:`swh.loader-pypi <swh-loader-pypi>`
-    loader for `PyPI <https://pypi.org/>`_ source code releases
-
 :ref:`swh.loader-svn <swh-loader-svn>`
     loader for `Subversion <https://subversion.apache.org/>`_ repositories
 
-:ref:`swh.loader-tar <swh-loader-tar>`
-    loader for source tarballs (including Tar, ZIP and other archive formats)
-
 :ref:`swh.model <swh-model>`
     implementation of the :ref:`data-model` to archive source code artifacts
 
@@ -139,7 +127,6 @@
    architecture
    getting-started
    developer-setup
-   manual-setup
    Infrastructure <infrastructure/index>
    API documentation <apidoc/modules>
    swh.core <swh-core/index>
diff --git a/docs/infrastructure/object_storage.rst b/docs/infrastructure/object_storage.rst
--- a/docs/infrastructure/object_storage.rst
+++ b/docs/infrastructure/object_storage.rst
@@ -66,6 +66,7 @@
 ====================
 
 .. graph:: swh_archives
+
 	"Main archive" -- "Replica archive";
 	"Azure archive";
 	"AWS archive";
diff --git a/docs/infrastructure/storage_site_rocquencourt_physical.rst b/docs/infrastructure/storage_site_rocquencourt_physical.rst
--- a/docs/infrastructure/storage_site_rocquencourt_physical.rst
+++ b/docs/infrastructure/storage_site_rocquencourt_physical.rst
@@ -5,7 +5,7 @@
 -----------
 
 The :doc:`hypervisors <hypervisors>` mostly use local storage on the form of internal
-SSDS but also have access to a :ref:`Ceph cluster`.
+SSDS but also have access to a :ref:`ceph_cluster`.
 
 NFS server
 ----------
diff --git a/docs/swh-loader.rst b/docs/swh-loader.rst
--- a/docs/swh-loader.rst
+++ b/docs/swh-loader.rst
@@ -7,10 +7,6 @@
    :titlesonly:
 
    swh.loader.core <swh-loader-core/index>
-   swh.loader.debian <swh-loader-debian/index>
-   swh.loader.dir <swh-loader-dir/index>
    swh.loader.git <swh-loader-git/index>
    swh.loader.mercurial <swh-loader-mercurial/index>
-   swh.loader.pypi <swh-loader-pypi/index>
    swh.loader.svn <swh-loader-svn/index>
-   swh.loader.tar <swh-loader-tar/index>
diff --git a/requirements-swh-dev.txt b/requirements-swh-dev.txt
--- a/requirements-swh-dev.txt
+++ b/requirements-swh-dev.txt
@@ -1,17 +1,21 @@
 # Add here internal Software Heritage dependencies, one per line.
--e ../swh-core[http,db]
+# Dependencies need to be ordered in a way that ensure only
+# development versions will be used (not the release ones hosted on PyPI).
+-e ../swh-core[http,db,logging]
+-e ../swh-model
+-e ../swh-objstorage[testing]
+-e ../swh-storage[schemata]
+-e ../swh-journal
+-e ../swh-scheduler
 -e ../swh-deposit
 -e ../swh-graph
+-e ../swh-icinga-plugins
 -e ../swh-indexer
--e ../swh-journal
 -e ../swh-lister
 -e ../swh-loader-core
 -e ../swh-loader-git
 -e ../swh-loader-mercurial
 -e ../swh-loader-svn
--e ../swh-model
--e ../swh-objstorage[testing]
--e ../swh-scheduler
--e ../swh-storage[schemata,listener]
+-e ../swh-search
 -e ../swh-vault
 -e ../swh-web
diff --git a/swh/docs/sphinx/conf.py b/swh/docs/sphinx/conf.py
--- a/swh/docs/sphinx/conf.py
+++ b/swh/docs/sphinx/conf.py
@@ -69,7 +69,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', 'swh-icinga-plugins/index.rst', 'swh-search/index.rst']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -96,7 +96,7 @@
     'sticky_navigation': True,
 }
 
-html_logo = 'software-heritage-logo-title-motto-vertical-white.png'
+html_logo = '_static/software-heritage-logo-title-motto-vertical-white.png'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,