diff --git a/cookbook/choose_protocol.ipynb b/cookbook/choose_protocol.ipynb
index 152014a..0b8ddb4 100644
--- a/cookbook/choose_protocol.ipynb
+++ b/cookbook/choose_protocol.ipynb
@@ -1,10 +1,17 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "0765a7c9",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_choose_config_protocol:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "8efbded0-0b69-4392-b8df-7afbd817d733",
    "metadata": {
-    "editable": true,
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@@ -35,7 +42,6 @@
    "execution_count": 1,
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@@ -50,7 +56,6 @@
    "cell_type": "markdown",
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@@ -64,7 +69,6 @@
    "cell_type": "markdown",
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@@ -89,7 +93,6 @@
    "execution_count": 2,
    "id": "b0757f5f-e38f-43ac-b43f-ee2bbea95f0d",
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@@ -108,7 +111,6 @@
    "cell_type": "markdown",
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@@ -130,7 +132,6 @@
    "cell_type": "markdown",
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@@ -145,7 +146,6 @@
    "execution_count": 3,
    "id": "96c32ead-a8d0-4283-950b-5d27c74ebf16",
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@@ -160,7 +160,6 @@
    "cell_type": "markdown",
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@@ -175,7 +174,6 @@
    "execution_count": 4,
    "id": "8d5a6281-50f9-4062-8fa4-375ce2df1bd6",
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@@ -250,7 +248,6 @@
    "cell_type": "markdown",
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@@ -265,7 +262,6 @@
    "execution_count": 5,
    "id": "2de6c6a9-bceb-4c9c-ae5a-3d88a72c801a",
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@@ -288,7 +284,6 @@
    "cell_type": "markdown",
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@@ -303,7 +298,6 @@
    "execution_count": 6,
    "id": "844e6fa5-f363-47fa-881d-00328faa601c",
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@@ -406,7 +400,6 @@
    "execution_count": 7,
    "id": "b499d852-4d7e-47c5-9342-31017baed37c",
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@@ -440,7 +433,6 @@
    "execution_count": 8,
    "id": "32b9b58a-d7ea-4071-9046-53e6990a1faa",
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@@ -476,7 +468,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
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diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
index 2186f7b..02f21c3 100644
--- a/cookbook/create_alchemical_network.ipynb
+++ b/cookbook/create_alchemical_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "9fb7586c",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_create_alchemicalnetwork:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "b89fdb9a-24fe-4aeb-9390-a359dae6cc9b",
@@ -22,7 +30,6 @@
    "cell_type": "markdown",
    "id": "471531a1-a351-413b-b147-794f9af4e0f8",
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@@ -109,7 +116,6 @@
    "execution_count": 4,
    "id": "d3054cfc-5040-4882-b3a3-92aba7ab5d1d",
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@@ -265,7 +271,6 @@
    "execution_count": 8,
    "id": "c9baa54c-513a-486a-a06a-fd8fd5d19fa5",
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@@ -284,7 +289,6 @@
    "cell_type": "markdown",
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@@ -298,7 +302,6 @@
    "cell_type": "markdown",
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@@ -315,7 +318,6 @@
    "execution_count": 9,
    "id": "2da4dafb-20d6-4ce7-ab83-4690528097d6",
    "metadata": {
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@@ -350,7 +352,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
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diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb
index 8580a05..8c615ef 100644
--- a/cookbook/generate_ligand_network.ipynb
+++ b/cookbook/generate_ligand_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "c6a2c302",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_planning_ligandnetwork:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "035c0099-6892-4ed2-b0d6-80b1c247c1e7",
@@ -259,7 +267,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.6"
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   "widgets": {
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diff --git a/cookbook/generate_lomap_network.ipynb b/cookbook/generate_lomap_network.ipynb
index 07183fe..cf3e586 100644
--- a/cookbook/generate_lomap_network.ipynb
+++ b/cookbook/generate_lomap_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "a41f6896",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_ligandnetwork_lomap:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "035c0099-6892-4ed2-b0d6-80b1c247c1e7",
diff --git a/cookbook/hand_write_ligand_network.ipynb b/cookbook/hand_write_ligand_network.ipynb
index 44eaaa5..e68a423 100644
--- a/cookbook/hand_write_ligand_network.ipynb
+++ b/cookbook/hand_write_ligand_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "554bc9f7",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_ligandnetworks_by_hand:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "bf739d70-3249-42b3-a352-8a41f8f8c667",
@@ -266,7 +274,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
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   "widgets": {
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diff --git a/cookbook/ligandnetwork_vis.ipynb b/cookbook/ligandnetwork_vis.ipynb
index f3e098f..57c0ac5 100644
--- a/cookbook/ligandnetwork_vis.ipynb
+++ b/cookbook/ligandnetwork_vis.ipynb
@@ -1,10 +1,17 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "68723119",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_viz_ligandnetworks:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "a2f0ee60-1060-4ca9-b0ff-529348dbc0e6",
    "metadata": {
-    "editable": true,
     "slideshow": {
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@@ -26,7 +33,6 @@
    "cell_type": "markdown",
    "id": "d4fe6c50-3971-4b9d-bc2f-71b5deb58fd4",
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@@ -41,7 +47,6 @@
    "execution_count": 1,
    "id": "aa30a8bc-bdf0-4382-98bd-2f33e703eb2d",
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@@ -71,7 +76,6 @@
    "execution_count": 2,
    "id": "594364f7-00ab-4497-bf5e-74cb497802e7",
    "metadata": {
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@@ -430,7 +434,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
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diff --git a/cookbook/loading_molecules.ipynb b/cookbook/loading_molecules.ipynb
index 045117c..9652244 100644
--- a/cookbook/loading_molecules.ipynb
+++ b/cookbook/loading_molecules.ipynb
@@ -4,7 +4,6 @@
    "cell_type": "raw",
    "id": "4d9beae7-b6bd-4743-9614-42450df0697d",
    "metadata": {
-    "editable": true,
     "raw_mimetype": "text/restructuredtext",
     "slideshow": {
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@@ -22,7 +21,6 @@
    "cell_type": "markdown",
    "id": "088a1bc4-e5f3-47ac-8ebf-1a904fa82f80",
    "metadata": {
-    "editable": true,
     "nbsphinx": "hidden",
     "slideshow": {
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@@ -37,7 +35,6 @@
    "cell_type": "raw",
    "id": "acb1ed05-1874-4dd3-a41d-e18623bece44",
    "metadata": {
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@@ -53,7 +50,6 @@
    "cell_type": "markdown",
    "id": "00d9ca69-1b38-4cf8-9c93-1fc4c08dae15",
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@@ -68,7 +64,6 @@
    "cell_type": "markdown",
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@@ -94,7 +89,6 @@
    "cell_type": "raw",
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@@ -112,7 +106,6 @@
    "cell_type": "markdown",
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@@ -127,7 +120,6 @@
    "cell_type": "markdown",
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@@ -142,7 +134,6 @@
    "execution_count": 1,
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@@ -163,7 +154,6 @@
    "cell_type": "markdown",
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@@ -179,7 +169,6 @@
    "cell_type": "markdown",
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@@ -195,7 +184,6 @@
    "execution_count": 2,
    "id": "7f7e56c9-2bee-46a1-9ccf-7003b4886249",
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@@ -213,7 +201,6 @@
    "cell_type": "markdown",
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@@ -233,7 +220,6 @@
    "execution_count": 3,
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@@ -257,7 +243,6 @@
    "cell_type": "raw",
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@@ -275,7 +260,6 @@
    "cell_type": "markdown",
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@@ -290,7 +274,6 @@
    "cell_type": "markdown",
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@@ -307,7 +290,6 @@
    "execution_count": 4,
    "id": "669ea0d6-3f49-4e91-b992-95f1bd5e7174",
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@@ -325,7 +307,6 @@
    "cell_type": "raw",
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@@ -343,7 +324,6 @@
    "cell_type": "markdown",
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@@ -358,7 +338,6 @@
    "cell_type": "markdown",
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@@ -375,7 +354,6 @@
    "execution_count": 5,
    "id": "e6c35e81-d0c9-4680-bb35-e7ae2b3fd2da",
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@@ -394,7 +372,6 @@
    "cell_type": "raw",
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@@ -412,7 +389,6 @@
    "cell_type": "markdown",
    "id": "1e388bd2-f1b3-4a90-970e-72b652f6227b",
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@@ -428,7 +404,6 @@
    "cell_type": "markdown",
    "id": "10655021-f3f0-4b21-9d8b-fc5a885555e4",
    "metadata": {
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@@ -447,7 +422,6 @@
    "execution_count": 6,
    "id": "bf52b73e-5705-48e7-b69a-fb63748588d8",
    "metadata": {
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@@ -491,7 +465,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
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diff --git a/cookbook/network_from_orion_fepp.ipynb b/cookbook/network_from_orion_fepp.ipynb
index 75744df..cf66146 100644
--- a/cookbook/network_from_orion_fepp.ipynb
+++ b/cookbook/network_from_orion_fepp.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "0508cde5",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_network_from_orion_fepp:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "4197d26d-c9e2-47ca-8d19-8372568371d8",
@@ -202,7 +210,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
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diff --git a/cookbook/rfe_alchemical_planners.ipynb b/cookbook/rfe_alchemical_planners.ipynb
index 7d94057..5c5c4ca 100644
--- a/cookbook/rfe_alchemical_planners.ipynb
+++ b/cookbook/rfe_alchemical_planners.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "6cf8c16b",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_rfe_network_planners:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "b89fdb9a-24fe-4aeb-9390-a359dae6cc9b",
diff --git a/cookbook/user_charges.ipynb b/cookbook/user_charges.ipynb
index cd470db..64ded3e 100644
--- a/cookbook/user_charges.ipynb
+++ b/cookbook/user_charges.ipynb
@@ -1,10 +1,17 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "9a5f5c39",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_user_charges:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "088a1bc4-e5f3-47ac-8ebf-1a904fa82f80",
    "metadata": {
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@@ -19,7 +26,6 @@
    "cell_type": "markdown",
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@@ -34,7 +40,6 @@
    "cell_type": "markdown",
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@@ -55,7 +60,6 @@
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@@ -150,7 +150,6 @@
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@@ -306,7 +300,7 @@
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