reinstate the nice already-expanded-to-one-level ToC sidebar with hea…

…dings. Remove now unused subdirectory index.rst files; shift any content in those to section overviews.
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diff --git a/docs/docs/Build Your Rig/index.rst → docs/docs/Build Your Rig/install-overview.md b/docs/docs/Build Your Rig/index.rst → docs/docs/Build Your Rig/install-overview.md
@@ -1,6 +1,4 @@
--------------------------------
-Installing OpenAPS on your rig
--------------------------------
+# Installing OpenAPS on your rig
 
 Getting OpenAPS running on your rig generally takes five steps:
 
@@ -21,16 +19,3 @@ Some conventions used in these docs:
 * You will see a <tt>$</tt> at the beginning of many of the lines of code. This
   indicates that it is to be entered and executed at the terminal prompt. Do not type in the dollar sign <tt>$</tt>.
 * Wherever there are `<bracketed_components>` in the code, these are meant for you to insert your own information. Most of the time, it doesn't matter what you choose **as long as you stay consistent throughout this guide**. That means if you choose `myedison` as your  `<edisonhostname>`, you must use `myedison` every time you see `<edisonhostname>`. Do not include the `< >` brackets in your commands when you enter them.  So for the example above, if the code snipped says `ssh root@<edisonhostname>.local`, you would enter `ssh root@myedison.local`
-
-
-
-.. toctree::
-   :maxdepth: 4
-   :hidden:
-
-   step-1-flashing
-   step-2-wifi-dependencies
-   step-3-setup-script
-   step-4-watching-log
-   step-5-finishing-setup
-   logging-into-rig-serial
diff --git a/docs/docs/Customize-Iterate/index.rst b/docs/docs/Customize-Iterate/index.rst
diff --git a/docs/docs/Gear Up/hardware-overview.md b/docs/docs/Gear Up/hardware-overview.md
@@ -0,0 +1,15 @@
+# Hardware overview
+
+This section describes the hardware components required for a 'typical' OpenAPS implementation. There are numerous variations and substitutions that can be made but the following items are recommended for getting started. 
+
+The basic setup requires:
+
+* a compatible insulin pump
+* a CGM
+* a small computer (Intel Edison, or Raspberry Pi for example) and a radio board/stick (i.e. Explorer Board for Edison or Explorer HAT for Pi)
+* a battery 
+
+If you come across something that doesn't seem to work, is no longer available, or if you have a notable alternative, feel free to edit this documentation with your suggestions.
+
+
+**Note about deprecated hardware setup:** Carelink can be used with up to oref0 0.6.2. However, it will not be used with oref0 0.7.0 moving forward. Carelink has poor range and will likely frustrate you. Please see the rig parts page for current hardware recommendations.
diff --git a/docs/docs/Gear Up/index.rst b/docs/docs/Gear Up/index.rst
diff --git a/docs/docs/Give Back-Pay It Forward/index.rst b/docs/docs/Give Back-Pay It Forward/index.rst
diff --git a/docs/docs/How it works/index.rst b/docs/docs/How it works/index.rst
diff --git a/docs/docs/Resources/index.rst b/docs/docs/Resources/index.rst
diff --git a/docs/docs/Resources/my-first-pr.md b/docs/docs/Resources/my-first-pr.md
@@ -1,4 +1,4 @@
-### Making your first PR (pull request)
+# Making your first PR (pull request)
 
 At some point it will be suggested that you make a PR. PR is short for pull request, and it is a way of adding or editing information stored in GitHub.  It's actually not too hard to do one and it is a great way to contribute. This documentation is here because people like you made PRs.  Don't worry about making a mistake or somehow editing the wrong documents.  There is always a review process before changes are merged into the "formal" OpenAPS documentation repository.  You can't mess up the originals through any accidents in the PR process.  The general process is:
 
@@ -33,7 +33,7 @@ Congrats, you made your first contribution!
 
 PS, your fork and branch will still be sitting on your own personal GitHub account. After you get a notification that your PR has been merged, you can delete your branch if you are done with it (Step 8's notification area will provide a link to delete the branch once it has been closed or merged). For future edits, if you follow this procedure the edits will always start with an updated version of the openaps repositories.  If you choose to use another method to start a PR request (e.g., editing starting from your forked repo's master branch as the starting point), you will need to ensure your repo is up-to-date by performing a "compare" first and merging in any updates that have happened since you last updated your fork.  Since people tend to forget to update their repos, we recommend using the PR process outlined above until you get familiar with performing "compares".
 
-### Advanced tips for adding multiple images to documentation
+## Advanced tips for adding multiple images to documentation
 
 If you are planning to make a lot of edits, including adding images to help illustrate parts of the documentation (thank you!), you may want to take the following approach:
 

diff --git a/docs/docs/Troubleshooting/General_linux_troubleshooting.md b/docs/docs/Troubleshooting/General_linux_troubleshooting.md
@@ -1,6 +1,8 @@
-# General Linux troubleshooting
+# Troubleshooting 
 
-## Before you get started
+Even those who follow this documentation precisely are bound to end up stuck at some point. This could be due to something unique to your system, a mistyped command, actions performed out of order, or even a typo in this guide. This section provides some tools to help diagnose the issue as well as some common errors that have been experienced and resolved before. If you get stuck, try re-reading the documentation again and after that, share what you've been working on, attempted steps to resolve, and other pertinent details in [#intend-to-bolus in Gitter](https://gitter.im/nightscout/intend-to-bolus) when asking for help troubleshooting. Here is also a [good blog post to read with tips on how to best seek help online to troubleshoot](https://diyps.org/2017/03/19/tips-for-troubleshooting-diy-diabetes-devices-openaps-or-otherwise/).
+
+## Introduction to using Linux
 
 Some familiarity with using the Terminal app (Mac computers) or Putty (Windows computers) will go a long way, but is not required for getting started.  Terminal (or PuTTY) is basically a portal into your rig, allowing us to use our computer's display and keyboard to communicate with the little [Edison or Pi] computer in your rig.  The active terminal line will show your current location, within the computer's file structure, where commands will be executed.  The line will end with a <tt>$</tt> and then have a prompt for you to enter your command.  
 

diff --git a/docs/docs/Troubleshooting/index.rst b/docs/docs/Troubleshooting/index.rst
diff --git a/docs/docs/Understanding OpenAPS-Overview/index.rst b/docs/docs/Understanding OpenAPS-Overview/index.rst
diff --git a/docs/docs/Usage and maintenance/index.rst b/docs/docs/Usage and maintenance/index.rst
diff --git a/docs/docs/While You Wait For Gear/index.rst b/docs/docs/While You Wait For Gear/index.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -19,27 +19,138 @@ This documentation supports a self-driven Do-It-Yourself (DIY) implementation of
 
    Additionally, it is equally important to only use original supplies such as inserters, cannulas and insulin containers approved by the manufacturer for use with your pump or CGM. Using untested or modified supplies can cause CGM inaccuracy and insulin dosing errors. Insulin is highly dangerous when misdosed - please do not play with your life by hacking with your supplies.
 
+
+
 .. toctree::
    :maxdepth: 2
    :glob:
    :hidden:
+   :caption: Overview
 
-   Overview: Understanding OpenAPS <docs/Understanding OpenAPS-Overview/index>
+   How OpenAPS works <docs/Understanding OpenAPS-Overview/how-openaps-works-overview>
+   Overview of steps <docs/Understanding OpenAPS-Overview/overview-of-build-process>
+   Using this documentation <docs/Understanding OpenAPS-Overview/using-the-docs>
+   Where to go for help <docs/Understanding OpenAPS-Overview/communication-support-channels>
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Hardware
+
+   Overview <docs/Gear Up/hardware-overview>
+   Compatible Pumps <docs/Gear Up/pump>
+   Compatible CGMs <docs/Gear Up/CGM>
+   Your rig hardware options <docs/Gear Up/rig-options> 
+   Edison rigs <docs/Gear Up/edison-explorer-board> 
+   Raspberry Pi rigs <docs/Gear Up/pi-based-rigs> 
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Getting ready
+
+   Set up Nightscout  <docs/While You Wait For Gear/nightscout-setup>
+   Collect your data & prepare <docs/While You Wait For Gear/collect-data-and-prepare>
+   Make your first PR <docs/While You Wait For Gear/loops-in-progress>
+   Do some reading <docs/While You Wait For Gear/reading-list>
 
-   Hardware <docs/Gear Up/index>
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Installing OpenAPS
 
-   Getting ready <docs/While You Wait For Gear/index>
-
-   Installing OpenAPS <docs/Build Your Rig/index>
+   Overview <docs/Build Your Rig/install-overview>
+   Step 1: Flashing<docs/Build Your Rig/step-1-flashing>
+   Step 2: Wifi and dependencies <docs/Build Your Rig/step-2-wifi-dependencies>
+   Step 3: Setup script <docs/Build Your Rig/step-3-setup-script>
+   Step 4: Watching logs <docs/Build Your Rig/step-4-watching-log>
+   Step 5: Finishing setup <docs/Build Your Rig/step-5-finishing-setup>
+   Logging into the rig using a serial connection <docs/Build Your Rig/logging-into-rig-serial>
+
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: How OpenAPS works
 
-   How OpenAPS works <docs/How it works/index>
+   How OpenAPS makes decisions  <docs/How it works/understand-determine-basal>
+   Insulin on board calculations <docs/How it works/understanding-insulin-on-board-calculations>
+   Understanding Autotune <docs/How it works/understanding-autotune>
+   Running Autotune <docs/How it works/autotune>
+   Using Autosens <docs/How it works/autosens>
 
-   Usage and maintenance <docs/Usage and maintenance/index>
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Usage and maintenance 
 
-   Customizing and extra features <docs/Customize-Iterate/index>
+	How to enter carbs and boluses <docs/Usage and maintenance/entering-carbs-bolus>
+   Preferences and safety settings <docs/Usage and maintenance/preferences-and-safety-settings>
+   Monitoring OpenAPS <docs/Usage and maintenance/monitoring-OpenAPS>
+   Using your loop: common situations <docs/Usage and maintenance/usability-considerations>
+   Optimizing your settings <docs/Usage and maintenance/optimize-your-settings>
+   How to run oref0-setup.sh again <docs/Usage and maintenance/oref0-runagain>
+   Update your rig in the future <docs/Usage and maintenance/update-your-rig>
+   Wifi options <docs/Usage and maintenance/Wifi/index>
 
-   Troubleshooting <docs/Troubleshooting/index>
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Customizing and extra features
+
+   oref1: SMB and UAM <docs/Customize-Iterate/oref1>
+   Useful apps for accessing your rig <docs/Customize-Iterate/useful-mobile-apps>
+   IFTTT and Pebble buttons <docs/Customize-Iterate/ifttt-integration>
+   Offline Looping <docs/Customize-Iterate/offline-looping-and-monitoring>
 
-   Give Back - Pay it Forward <docs/Give Back-Pay It Forward/index>
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Troubleshooting
 
-   Resources <docs/Resources/index>
+   Overview and Linux reference <docs/Troubleshooting/General_linux_troubleshooting>
+   oref0-setup Troubleshooting<docs/Troubleshooting/oref0-setup-troubleshooting
+   Common error messages <docs/Troubleshooting/Common-error-messages>
+   Wifi and hotspot issues <docs/Troubleshooting/Wifi-and-hotspot-issues>
+   Pump-rig communications troubleshooting <docs/Troubleshooting/Pump-rig-communications-troubleshooting>
+   CGM-rig communications troubleshooting <docs/Troubleshooting/CGM-rig-communications-troubleshooting>
+   NS-rig communications troubleshooting<docs/Troubleshooting/Rig-NS-communications-troubleshooting>
+   Medtronic button errors <docs/Troubleshooting/Medtronic-Button-Errors>
+   Carelink troubleshooting <docs/Troubleshooting/Carelink>
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Give Back-Pay It Forward
+
+   Donate your data <docs/Give Back-Pay It Forward/data-commons-data-donation>
+   Help others - pay it forward <docs/Give Back-Pay It Forward/contribute>
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+   :hidden:
+   :caption: Resources/Reference
+
+   For Clinicians <docs/Resources/clinician-guide-to-OpenAPS>
+   History <docs/Resources/history>
+   Glossary <docs/Resources/glossary>
+   Making a PR <docs/Resources/my-first-pr>
+   Technical resources <docs/Resources/technical-resources>
+   Switching between DIY systems <docs/Resources/switching-between-DIY-systems>
+   <docs/Resources/Deprecated: Pi Hardware info <Deprecated-Pi/Pi-hardware>
+   <docs/Resources/Deprecated: Pi Setup info <Deprecated-Pi/Pi-setup>
+
+
+
+
+
+