more docs

16 files changed, 520 insertions, 211 deletions

diff --git a/docs/source/adc.rst b/docs/source/adc.rst
index 17c672d..4e118aa 100644
--- a/docs/source/adc.rst
+++ b/docs/source/adc.rst
@@ -4,4 +4,72 @@
  ADC
 =====
 
-Stub.
+Analog-Digital Conversion is the process of reading a physical voltage
+as a number. The Maple has a large number of pins which are capable of
+taking 12-bit ADC measurements, which means that voltages from ground
+to +3.3v are read as numbers from 0 to 4095; this corresponds to a
+theoretical sensitivity of just under 1 millivolt. In reality, a
+number of factors introduce noise and bias into this reading and a
+number of techniques must be used to get good precision and accuracy.
+
+.. compound::
+
+   The header pins with ADC functionality (marked as "AIN" on the
+   silkscreen) are:
+
+     D0, D1, D2, D3, D10, D11, D12, D13, D15, D16, D17, D18, D19, D20, D27, D28
+
+.. contents:: Contents
+   :local:
+
+.. _adc-noise-bias:
+
+Noise and Bias
+--------------
+
+The biggest issues with analog-digital conversion are noise and bias.
+With the Maple, we have tried to isolate the ADC pins and traces from
+strong noise sources but there are always trade--offs between noise,
+additional functionality, cost, and package size.
+
+The 6 ADC pins in a bank (D15--D20) generally have the least
+noise and should be used for fine measurements.  If the input voltage
+changes relatively slowly, a number of samples can be taken in
+succession and averaged together, or the same voltage can even be
+sampled by multiple ADC pins at the same time.
+
+An important factor when taking a voltage reading is the reference
+voltages that the sample is being compared against. In the case of the
+Maple, the high reference is |vcc| and the low reference is ground.
+This means that noise or fluctuations on either |vcc| or ground will
+affect the measurement. It also means that the voltage you are trying
+to sample must be between ground and 3.3V. In the case of a variable
+reading, it is best if the voltage varies over the entire range of
+0--3.3V; otherwise, only a fraction of the sensitivity is being
+leveraged.  Resistor dividers and constant voltage diodes are basic
+tools which can help bring a given voltage signal into the appropriate
+range; opamps and other powered components can also be used.
+
+.. _adc-function-reference:
+
+Function Reference
+------------------
+
+.. TODO function reference (figure out Doxygen first)
+
+.. _adc-recommended-reading:
+
+Recommended Reading
+-------------------
+
+* `Wikipedia article on Analog-to-digital converter <http://en.wikipedia.org/wiki/Analog-to-digital_converter>`_
+* `Arduino Analog Input Tutorial <http://arduino.cc/en/Tutorial/AnalogInputPins>`_
+* STMicro documentation for STM32F103RB microcontroller:
+
+  * `All <http://www.st.com/mcu/devicedocs-STM32F103RB-110.html>`_
+  * `Datasheet (pdf) <http://www.st.com/stonline/products/literature/ds/13587.pdf>`_
+  * `Reference Manual (pdf) <http://www.st.com/stonline/products/literature/rm/13902.pdf>`_
+  * `Application Note on ADC Modes (pdf) <http://www.st.com/stonline/products/literature/an/16840.pdf>`_
+  * `Application Note on ADC Oversampling (pdf) <http://www.st.com/stonline/products/literature/an/14183.pdf>`_
+
+
diff --git a/docs/source/bootloader.rst b/docs/source/bootloader.rst
index 9280c68..c4c5da2 100644
--- a/docs/source/bootloader.rst
+++ b/docs/source/bootloader.rst
@@ -15,6 +15,9 @@ Flash memory and only runs when the chip is reset).
 
 **Visit the github development project**: http://github.com/leaflabs/maple-bootloader
 
+.. contents:: Contents
+   :local:
+
 Bootloader Schemes Explained!
 -----------------------------
 
diff --git a/docs/source/compatibility.rst b/docs/source/compatibility.rst
index aeed36b..6166ec5 100644
--- a/docs/source/compatibility.rst
+++ b/docs/source/compatibility.rst
@@ -1,7 +1,136 @@
+.. highlight:: cpp
+
 .. _compatibility:
 
 =============================
  Maple-Arduino Compatibility
 =============================
 
+.. contents:: Contents
+   :local:
+
+Overview
+--------
+
+The biggest difference between the Maple and most Arduino boards is
+that the Maple uses a 32-bit ARM Cortex-M3 architecture chip while the
+Arduinos have 8-bit Atmel AVR chips. The different instruction set
+means that machine code (executable binary programs) is incompatible
+between the two, and a different compiler (actually just a different
+version of `gcc <http://gcc.gnu.org/>`_) is required. The compiler for
+the regular Arduino IDE is the popular :command:`avr-gcc` package; the
+compiler for the Maple version of the IDE is CodeSourcery's edition of
+gcc for the ARM EABI target (:command:`arm-non-eabi-gcc`).
+
+The bitwidth of the processor means that the Maple can process 32-bit
+operations (like adding two 32-bit integers) in a single instruction,
+while an Arduino processor would have to split up large operations
+into several smaller ones. In a lot of cases 8-bit operations are
+plenty (integers 0-255, single characters of text, etc.), but if
+you're dealing with higher resolution data, the speed up could be
+significant. A trade-off is that code could be larger as well; program
+instructions and memory locations can be up to 32-bits each, which in
+the worst case would quadruple program size. In reality, the removal
+of extra instructions and fancy packing together of simple
+instructions means that programs aren't much larger (or are even
+smaller).
+
+Header Numbering and Incompatibilities
+--------------------------------------
+
+The numbering of headers is different; on the Maple each GPIO has a
+unique number: D0, D1, D2, all the way up to D37 (actually, there are
+:ref:`a few more <jtag>`...). On the Arduino, the analog pins are
+numbered separately (A0-A5) from the digital pins (D0\ -D13).
+
+The incompatible hardware differences are:
+
+* |i2c| port: on most Arduinos, the |i2c| port is Analog Input
+  4 (SDA) and Analog Input 5 (SCL); on the Maple, |i2c| port 1 is D5
+  (SCL) and D9 (SDA), and |i2c| port 2 is D29 (SCL) and D30 (SDA).
+
+  It should be possible to skywire, sacrificing signal quality (due to
+  increased capacitance). Alternatively, |i2c| can be bit-banged
+  reasonably well in software. This peripheral could potentially be
+  rerouted internally, but we haven't looked into it.
+
+* :ref:`PWM <pwm>` on D10: all the other standard Arduino PWM headers have PWM
+  functionality on the Maple (D2,D3,D6,D9,D11), but not D10. We did
+  our best! It may be possible to reroute this peripheral internally
+  using low level configuration, but we haven't looked in to it.
+
+* No External Voltage Reference: The Arduino has an Aref pin which
+  allows the use of an external ADC voltage reference; the Maple has
+  an extra GPIO pin (14) with PWM capability in this spot, and does
+  not allow an external voltage reference to be configured.
+
+* EEPROM: the Maple does not have any internal EEPROM. This
+  functionality can be emulated with regular persistent flash memory,
+  or with an external EEPROM chip.
+
+* ISP Programming: the Maple does not use an ISP/ICSP bus for
+  debugging; it uses :ref:`JTAG <jtag>`.
+
+
+Software Language/Library Changes
+---------------------------------
+
+With :ref:`one notable exception <language-no-word>`, the entire
+Arduino language is supported.  However, there are some subtle
+differences, most of which are improvements:
+
+* 32-bit integers: many standard functions either expect or return
+  full 32-bit (4 byte) integer values instead of the regular 16-bit (2
+  byte) Arduino values.
+
+* `pinMode()`_ types: any :ref:`GPIO <gpio>` (including analog pins)
+  can be configured into one of the following modes with a single call
+  to `pinMode()`_: ``OUTPUT``, ``OUTPUT_OPEN_DRAIN``,
+  ``INPUT_FLOATING``, ``INPUT_PULLUP``,
+  ``INPUT_PULLDOWN``. Additionally, the PWM and Analog Input pins can
+  be configured as ``INPUT_ANALOG`` and ``PWM`` respectively. See the
+  :ref:`GPIO documentation <gpio>` for more information.
+
+  .. TODO: reference libmaple docs above when they're done
+
+* Serial1 syntax: like the `Arduino Mega
+  <http://arduino.cc/en/Main/ArduinoBoardMega>`_, the Maple has
+  multiple USART ports.  By default, Serial is not mapped to any of
+  them, use ``Serial1`` through ``Serial3`` instead.
+
+  .. TODO: reference libmaple docs for Serial[n] above when they're done
+
+* 16-bit :ref:`PWM <pwm>`: Arduino boards support 8-bit PWM, which
+  means that calls to `analogWrite()`_ take values between 0 (always
+  off) and 255 (always on).  The Maple supports 16-bit PWM, so the
+  corresponding values should be between 0 (always off) and 65535
+  (always on).
+
+* 12-bit :ref:`ADC <adc>`: Arduino boards support 10-bit ADC, which
+  means that calls to `analogRead()`_ will return values between 0 and
+  1023.  The Maple supports 12-bit ADC, so the same call will instead
+  return values between 0 and 4095.
+
+
+.. class:: ported-feature
+
+I am supported!
+
+This should be ordinary
+
+.. class:: non-ported-feature
+
+I can't do it :(
+
+Also ordinary
+
+.. class:: partly-ported-feature
+
+I sorta work
+
+And I am also ordinary
+
 Stub.
+
+(not finished)
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 5fcb939..26147fd 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -17,7 +17,11 @@ import sys, os
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+#
+# We rely on Michael Jones's breathe as a Doxygen-to-Sphinx bridge.
+# See libmaple/docs/README for information on obtaining it and letting
+# Sphinx know where it is.
+sys.path.append(os.environ['BREATHE_HOME'])
 
 # -- General configuration ----------------------------------------------------
 
@@ -29,7 +33,7 @@ import sys, os
 # ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
               'sphinx.ext.intersphinx', 'sphinx.ext.todo',
-              'sphinx.ext.coverage']
+              'sphinx.ext.coverage', 'breathe']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -68,12 +72,16 @@ release = '0.0.7'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['epilog.rst']
+exclude_patterns = ['epilog.rst', 'prolog.rst']
 
 # Included at the end of every source file that is read.
 with open('epilog.rst', 'r') as ep:
     rst_epilog = ep.read()
 
+# Included at the beginning of every source file that is read.
+with open('prolog.rst', 'r') as pr:
+    rst_prolog = pr.read()
+
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
 #default_role = None
@@ -229,3 +237,11 @@ man_pages = [
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'http://docs.python.org/': None}
+
+
+# -- Options for breathe integration ------------------------------------------
+
+breathe_projects = {'libmaple' : os.path.join(os.environ['LIB_MAPLE_HOME'],
+                                              'docs', 'doxygen', 'xml')}
+
+breathe_default_project = 'libmaple'
diff --git a/docs/source/epilog.rst b/docs/source/epilog.rst
index 0e430c8..7805362 100644
--- a/docs/source/epilog.rst
+++ b/docs/source/epilog.rst
@@ -4,5 +4,56 @@
 .. Common URL references
 .. _forum: http://forums.leaflabs.com
 .. _contact: http://leaflabs.com/contact/
+
+
+.. Arduino built-in functions
 .. _setup(): http://arduino.cc/en/Reference/Setup
 .. _loop(): http://arduino.cc/en/Reference/Loop
+
+.. _pinMode(): http://arduino.cc/en/Reference/PinMode
+.. _digitalWrite(): http://arduino.cc/en/Reference/DigitalWrite
+.. _digitalRead(): http://arduino.cc/en/Reference/DigitalRead
+
+.. _analogReference(): http://arduino.cc/en/Reference/AnalogReference
+.. _analogRead(): http://arduino.cc/en/Reference/AnalogRead
+.. _analogWrite(): http://arduino.cc/en/Reference/AnalogWrite
+
+.. _tone(): http://arduino.cc/en/Reference/Tone
+.. _noTone(): http://arduino.cc/en/Reference/NoTone
+.. _shiftOut(): http://arduino.cc/en/Reference/ShiftOut
+.. _pulseIn(): http://arduino.cc/en/Reference/PulseIn
+
+.. _millis(): http://arduino.cc/en/Reference/Millis
+.. _micros(): http://arduino.cc/en/Reference/Micros
+.. _delay(): http://arduino.cc/en/Reference/Delay
+.. _delayMicroseconds(): http://arduino.cc/en/Reference/DelayMicroseconds
+
+.. _min(): http://arduino.cc/en/Reference/Min
+.. _max(): http://arduino.cc/en/Reference/Max
+.. _abs(): http://arduino.cc/en/Reference/Abs
+.. _constrain(): http://arduino.cc/en/Reference/Constrain
+
+.. _map(): http://arduino.cc/en/Reference/Map
+.. _pow(): http://arduino.cc/en/Reference/Pow
+.. _sqrt(): http://arduino.cc/en/Reference/Sqrt
+
+.. _sin(): http://arduino.cc/en/Reference/Sin
+.. _cos(): http://arduino.cc/en/Reference/Cos
+.. _tan(): http://arduino.cc/en/Reference/Tan
+
+.. _randomSeed(): http://arduino.cc/en/Reference/RandomSeed
+.. _random(): http://arduino.cc/en/Reference/Random
+
+.. _lowByte(): http://arduino.cc/en/Reference/LowByte
+.. _highByte(): http://arduino.cc/en/Reference/HighByte
+.. _bitRead(): http://arduino.cc/en/Reference/BitRead
+.. _bitWrite(): http://arduino.cc/en/Reference/BitWrite
+.. _bitSet(): http://arduino.cc/en/Reference/BitSet
+.. _bitClear(): http://arduino.cc/en/Reference/BitClear
+.. _bit(): http://arduino.cc/en/Reference/Bit
+
+.. _attachInterrupt(): http://arduino.cc/en/Reference/AttachInterrupt
+.. _detachInterrupt(): http://arduino.cc/en/Reference/DetachInterrupt
+
+.. _interrupts(): http://arduino.cc/en/Reference/Interrupts
+.. _noInterrupts(): http://arduino.cc/en/Reference/NoInterrupts
diff --git a/docs/source/errata.rst b/docs/source/errata.rst
index b702bd1..09b2ad1 100644
--- a/docs/source/errata.rst
+++ b/docs/source/errata.rst
@@ -4,4 +4,15 @@
  Errata
 ========
 
+This page is a collection of known issues and warnings for each
+revision of the Maple board. The failure modes aren't design errors,
+but are easy ways to break or damage your board permanently. For a
+list of differences between the Maple and Arduinos, see the page on
+:ref:`compatibility <compatibility>`.
+
+.. contents:: Contents
+   :local:
+
 Stub.
+
+(not finished)
diff --git a/docs/source/gpio.rst b/docs/source/gpio.rst
index f608a61..2567221 100644
--- a/docs/source/gpio.rst
+++ b/docs/source/gpio.rst
@@ -4,4 +4,91 @@
  GPIO
 ======
 
-Stub.
+The Maple features 38 ready-to-use general purpose input/output (GPIO)
+pins for digital input/output, numbered D0 through D37.  These numbers
+correspond to the numeric values next to each header on the Maple
+silkscreen.
+
+Many of these pins may additionally be used for special features or
+peripheral functions.  This page documents those capabilities, by pin.
+
+The current and voltage limitations have not been copied over from the
+STM32 datasheet (see the :ref:`Recommended Reading
+<gpio-recommended-reading>` for a link).  In particular, a number of
+GPIO pins are 5v tolerant (which means that applying 5v to a pin and
+reading it as input or allowing it to drain to ground will not damage
+that pin), while some are not.
+
+.. contents:: Contents
+   :local:
+
+Pin Mapping Mega Table
+----------------------
+
+This huge reference table shows the available functionality on every
+GPIO pin, by peripheral type. The "STM32" column refers to the port
+and number that the header is connected to on the microcontroller.
+The "5v?" column documents whether or not the pin is 5v tolerant (see
+above).
+
+.. csv-table::
+   :header: "Pin", "STM32", ":ref:`ADC <adc>`", ":ref:`Timer <timers>`", ":ref:`I2C <i2c>`", ":ref:`UART <usart>`", ":ref:`SPI <spi>`", "5v?"
+
+   "D0",  "PA3",  "ADC3", "TIM2_CH4",     "-",         "USART2_RX",  "-",         "No"
+   "D1",  "PA2",  "ADC2", "TIM2_CH3",     "-",         "USART2_TX",  "-",         "No"
+   "D2",  "PA0",  "ADC0", "TIM2_CH1_ETR", "-",         "USART2_CTS", "-",         "No"
+   "D3",  "PA1",  "ADC1", "TIM2_CH2",     "-",         "USART2_RTS", "-",         "No"
+   "D4",  "PB5",  "-",    "-",            "ISC1_SMBA", "-",          "-",         "No"
+   "D5",  "PB6",  "-",    "TIM4_CH1",     "I2C1_SCL",  "-",          "-",         "Yes"
+   "D6",  "PA8",  "-",    "TIM1_CH1",     "-",         "USART1_CK",  "-",         "Yes"
+   "D7",  "PA9",  "-",    "TIM1_CH2",     "-",         "USART1_TX",  "-",         "Yes"
+   "D8",  "PA10", "-",    "TIM1_CH3",     "-",         "USART1_RX",  "-",         "Yes"
+   "D9",  "PB7",  "-",    "TIM4_CH2",     "I2C1_SDA",  "-",          "-",         "Yes"
+   "D10", "PA4",  "ADC4", "-",            "-",         "USART2_CK",  "SPI1_NSS",  "No"
+   "D11", "PA7",  "ADC7", "TIM3_CH2",     "-",         "-",          "SPI1_MOSI", "No"
+   "D12", "PA6",  "ADC6", "TIM3_CH1",        -       -       SPI1_MISO       No
+   D13  PA5     ADC5    -       -       -       SPI1_SCK        No
+   D14  PB8     -       TIM4_CH3        -       -       -       Yes
+
+   Analog header
+
+   D15  PC0     ADC10   -       -       -       -       No
+   D16  PC1     ADC11   -       -       -       -       No
+   D17  PC2     ADC12   -       -       -       -       No
+   D18  PC3     ADC13   -       -       -       -       No
+   D19  PC4     ADC14   -       -       -       -       No
+   D20  PC5     ADC15   -       -       -       -       No
+
+   External header
+
+   D21  PC13    -       -       -       -       -       No
+   D22  PC14    -       -       -       -       -       No
+   D23  PC15    -       -       -       -       -       No
+   D24  PB9     -       TIM4_CH4        -       -       -       Yes
+   D25  PD2     -       TIM3_ETR        -       -       -       Yes
+   D26  PC10    -       -       -       -       -       Yes
+   D27  PB0     ADC8    TIM3_CH3        -       -       -       No
+   D28  PB1     ADC9    TIM3_CH4        -       -       -       No
+   D29  PB10    -       -       I2C2_SCL        USART3_TX       -       Yes
+   D30  PB11    -       -       I2C2_SDA        USART3_RX       -       Yes
+   D31  PB12    -       TIM1_BKIN       I2C2_SMBAL      USART3_CK       SPI2_NSS        Yes
+   D32  PB13    -       TIM1_CH1N       -       USART3_CTS      SPI2_SCK        Yes
+   D33  PB14    -       TIM1_CH2N       -       USART3_RTS      SPI2_MISO       Yes
+   D34  PB15    -       TIM1_CH3N       -       -       SPI2_MOSI       Yes
+   D35  PC6     -       -       -       -       -       Yes
+   D36  PC7     -       -       -       -       -       Yes
+   D37  PC8     -       -       -       -       -       
+
+
+Stub (unfinished).
+
+.. _gpio-recommended-reading:
+
+Recommended Reading
+-------------------
+
+STMicro documentation for STM32F103RB microcontroller:
+
+  * `All <http://www.st.com/mcu/devicedocs-STM32F103RB-110.html>`_
+  * `Datasheet (pdf) <http://www.st.com/stonline/products/literature/ds/13587.pdf>`_
+  * `Reference Manual (pdf) <http://www.st.com/stonline/products/literature/rm/13902.pdf>`_
diff --git a/docs/source/i2c.rst b/docs/source/i2c.rst
index e0444eb..34bd57c 100644
--- a/docs/source/i2c.rst
+++ b/docs/source/i2c.rst
@@ -4,6 +4,4 @@
 |i2c|
 =====
 
-.. |i2c| replace:: I\ :sup:`2`\ C
-
 Stub.
diff --git a/docs/source/language.rst b/docs/source/language.rst
index 8115d6b..6eb5bc7 100644
--- a/docs/source/language.rst
+++ b/docs/source/language.rst
@@ -24,6 +24,9 @@ C or C++ programmers curious about the differences between the Wiring
 language and C++ may wish to skip to the
 :ref:`arduino_c_for_c_hackers`.
 
+.. contents:: Contents
+   :local:
+
 Unique Maple Additions
 ----------------------
 
@@ -308,59 +311,15 @@ Arduino Documentation Links
 .. _const: http://arduino.cc/en/Reference/Const
 .. _sizeof(): http://arduino.cc/en/Reference/Sizeof
 
-.. _pinMode(): http://arduino.cc/en/Reference/PinMode
-.. _digitalWrite(): http://arduino.cc/en/Reference/DigitalWrite
-.. _digitalRead(): http://arduino.cc/en/Reference/DigitalRead
-
-.. _analogReference(): http://arduino.cc/en/Reference/AnalogReference
-.. _analogRead(): http://arduino.cc/en/Reference/AnalogRead
-.. _analogWrite(): http://arduino.cc/en/Reference/AnalogWrite
-
-.. _tone(): http://arduino.cc/en/Reference/Tone
-.. _noTone(): http://arduino.cc/en/Reference/NoTone
-.. _shiftOut(): http://arduino.cc/en/Reference/ShiftOut
-.. _pulseIn(): http://arduino.cc/en/Reference/PulseIn
-
-.. _millis(): http://arduino.cc/en/Reference/Millis
-.. _micros(): http://arduino.cc/en/Reference/Micros
-.. _delay(): http://arduino.cc/en/Reference/Delay
-.. _delayMicroseconds(): http://arduino.cc/en/Reference/DelayMicroseconds
-
-.. _min(): http://arduino.cc/en/Reference/Min
-.. _max(): http://arduino.cc/en/Reference/Max
-.. _abs(): http://arduino.cc/en/Reference/Abs
-.. _constrain(): http://arduino.cc/en/Reference/Constrain
-
-.. _map(): http://arduino.cc/en/Reference/Map
-.. _pow(): http://arduino.cc/en/Reference/Pow
-.. _sqrt(): http://arduino.cc/en/Reference/Sqrt
-
-.. _sin(): http://arduino.cc/en/Reference/Sin
-.. _cos(): http://arduino.cc/en/Reference/Cos
-.. _tan(): http://arduino.cc/en/Reference/Tan
-
-.. _randomSeed(): http://arduino.cc/en/Reference/RandomSeed
-.. _random(): http://arduino.cc/en/Reference/Random
-
-.. _lowByte(): http://arduino.cc/en/Reference/LowByte
-.. _highByte(): http://arduino.cc/en/Reference/HighByte
-.. _bitRead(): http://arduino.cc/en/Reference/BitRead
-.. _bitWrite(): http://arduino.cc/en/Reference/BitWrite
-.. _bitSet(): http://arduino.cc/en/Reference/BitSet
-.. _bitClear(): http://arduino.cc/en/Reference/BitClear
-.. _bit(): http://arduino.cc/en/Reference/Bit
-
+.. Links for the standard Arduino built-in functions are included as
+.. part of the standard epilog.
 .. _our reference page: http://leaflabs.com/docs/external-interrupts/
-.. _attachInterrupt(): http://arduino.cc/en/Reference/AttachInterrupt
-.. _detachInterrupt(): http://arduino.cc/en/Reference/DetachInterrupt
-
-.. _interrupts(): http://arduino.cc/en/Reference/Interrupts
-.. _noInterrupts(): http://arduino.cc/en/Reference/NoInterrupts
 
 .. _Serial: http://arduino.cc/en/Reference/Serial
 .. _community-contributed code: http://www.arduino.cc/playground/Main/GeneralCodeLibrary
 .. _newlib: http://sourceware.org/newlib/
 
+
 .. _arduino_c_for_c_hackers:
 
 Note for C/C++ Programmers
diff --git a/docs/source/libmaple-api.rst b/docs/source/libmaple-api.rst
index af283cb..d5b90b6 100644
--- a/docs/source/libmaple-api.rst
+++ b/docs/source/libmaple-api.rst
@@ -8,3 +8,4 @@ This page documents the lower-level features of libmaple, which may be
 of use to programmers who don't wish to use the Arduino-style
 environment provided by the `Maple IDE <maple-ide-install>`_.
 
+Stub.
diff --git a/docs/source/libmaple.rst b/docs/source/libmaple.rst
index 620fdfa..a018cd7 100644
--- a/docs/source/libmaple.rst
+++ b/docs/source/libmaple.rst
@@ -30,6 +30,8 @@ wrappers and code to imitate the Arduino programming library.
 
     git clone git://github.com/leaflabs/libmaple.git
 
+**Table of contents:**
+
 .. toctree::
    :maxdepth: 2
 
diff --git a/docs/source/libraries.rst b/docs/source/libraries.rst
index c2d5cb0..6a97b0e 100644
--- a/docs/source/libraries.rst
+++ b/docs/source/libraries.rst
@@ -15,8 +15,8 @@ library you want.
 Any incompatibilities between the Maple and Arduino versions are noted
 in the description of the library.
 
-* :ref:`LiquidCrystal <liquid_crystal>`
-* :ref:`Wire <wire>`
+.. contents:: Contents
+   :local:
 
 .. _liquid_crystal:
 
diff --git a/docs/source/maple-ide-install.rst b/docs/source/maple-ide-install.rst
index 46c903b..3c3fffe 100644
--- a/docs/source/maple-ide-install.rst
+++ b/docs/source/maple-ide-install.rst
@@ -11,7 +11,8 @@ check the :ref:`troubleshooting page <troubleshooting>` for help with
 some common problems. If all else fails, try our `forum`_, or `contact
 us directly <http://leaflabs.com/contact>`_!
 
-.. _forum: http://forums.leaflabs.com
+.. contents:: Contents
+   :local:
 
 Download
 --------
diff --git a/docs/source/maple-quickstart.rst b/docs/source/maple-quickstart.rst
index 20d84a0..4d646d7 100644
--- a/docs/source/maple-quickstart.rst
+++ b/docs/source/maple-quickstart.rst
@@ -15,13 +15,8 @@ If you have trouble along the way, try the :ref:`troubleshooting page
 <troubleshooting>` for help with some common problems.  If all else
 fails, try our `forum`_, or `contact us directly <contact>`_!
 
-The steps are:
-
-* :ref:`Install and run the IDE <maple-quickstart-get-ide>`
-
-* :ref:`Compile and upload a program <maple-quickstart-compile-blinky>`
-
-* :ref:`Test the USB serial connection <maple-quickstart-serial-port>`
+.. contents:: Contents
+   :local:
 
 .. _maple-quickstart-get-ide:
 
diff --git a/docs/source/prolog.rst b/docs/source/prolog.rst
new file mode 100644
index 0000000..2823947
--- /dev/null
+++ b/docs/source/prolog.rst
@@ -0,0 +1,7 @@
+.. Additions to this file will be included at the beginning of every
+.. .rst file.  DO NOT USE IT to insert a header; this is not
+.. recommended by the Sphinx people, who have other ways of doing it.
+
+.. Common substitutions
+.. |vcc| replace:: V\ :sub:`cc`
+.. |i2c| replace:: I\ :sup:`2`\ C
diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index b878ae4..9d452d1 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -2,231 +2,212 @@
 
 .. _troubleshooting:
 
-=======================
- Maple Troubleshooting
-=======================
-
-* :ref:`Hardware Problems <troubleshooting-hardware>`
-
-  * The status LED is throbbing and I can't upload my program!
-  * My board is bricked! I can't upload via the bootloader no matter what!
-  * My 5v peripheral doesn't work! (I2C, SPI, USART, etc)
-  * The reset and D38/serial buttons don't seem to work reliably!
-
-* :ref:`IDE installation problems <troubleshooting-ide-install>`
-
-  * I don't have root/administrator access!
-  * [Linux] I don't use udev!
-
-* :ref:`IDE usage problems <troubleshooting-ide-usage>`
-
-  * [Mac OSX] The "Board" and "Serial Port" menu items are missing!
-
-* :ref:`Common compiler problems <troubleshooting-compilation>`
-
-  * ``NullPointerException``
-  * ``undefined reference to setup()/loop()``
-  * ``error: 'Serial' was not declared in this scope``
-  * ``File(s) not found``
-
-* :ref:`Common upload problems <troubleshooting-upload>`
-
-  * My program is too large!
-  * ``No DFU capable USB device found``
-  * I have multiple Maples installed; how do I know which one will get flashed?
+Troubleshooting
+===============
 
-* :ref:`Command-line issues <troubleshooting-shell>`
+This page documents common problems and their solutions.
 
-  * My flash programs don't seem to stick; they behave like they are RAM!
-  * [Linux] ``cdc_acm 3-1:1.0: no more free acm devices``
+.. contents:: Contents
+   :local:
 
-* :ref:`Tips and tricks <troubleshooting-tips-tricks>`
-
-  * Perpetual bootloader mode
-
-.. _troubleshooting-hardware:
-
-Hardware problems
------------------
+===================
+ Hardware problems
+===================
 
 The status LED is throbbing and I can't upload my program!
+----------------------------------------------------------
 
-    The LED throbs when there has been a failed software
-    :ref:`assertion <language-assert>`.
+The LED throbs when there has been a failed software :ref:`assertion
+<language-assert>`.
 
-    You can still reprogram by resetting the board and uploading
-    during the short window when the bootloader waits for a
-    program.
+You can still reprogram by resetting the board and uploading during
+the short window when the bootloader waits for a program.
 
-    To make this window longer (it can be hard to get the timing
-    right), use :ref:`perpetual bootloader mode
-    <troubleshooting-perpetual-bootloader>`.
+To make this window longer (it can be hard to get the timing right),
+use :ref:`perpetual bootloader mode
+<troubleshooting-perpetual-bootloader>`.
 
 My board is bricked! I can't upload via the bootloader no matter what!
+----------------------------------------------------------------------
 
-    Use the hardcoded serial STM32 serial bootloader to re-flash the
-    bootloader.
+Use the hardcoded serial STM32 serial bootloader to re-flash the
+bootloader.
 
-    .. TODO insert docs on reflashing the bootloader
+.. TODO insert docs on reflashing the bootloader
 
-    If it really is bricked, and you think it's our fault,
-    `contact us <http://leaflabs.com/contact>`_\ !
+If it really is bricked, and you think it's our fault, `contact us
+<http://leaflabs.com/contact>`_\ !
 
 My 5v peripheral doesn't work! (I2C, SPI, USART, etc)
+-----------------------------------------------------
 
-    Yup, the Maple is a 3.3v board. You may need to use a level
-    converter. See the :ref:`compatibility <compatibility>`,
-    :ref:`GPIO <gpio>`, or other :ref:`hardware specific documentation
-    <hardware>` for more information.
+Yup, the Maple is a 3.3v board. You may need to use a level
+converter. See the :ref:`compatibility <compatibility>`, :ref:`GPIO
+<gpio>`, or other :ref:`hardware specific documentation <hardware>`
+for more information.
 
 The reset and D38/serial buttons don't seem to work reliably!
+-------------------------------------------------------------
 
-    A few rev3 boards shipped in May-June 2010 may have had unreliable
-    buttons; see the :ref:`errata page <errata>` for details.  `We're
-    happy to replace these for you <http://leaflabs.com/contact>`_\ !
+A few rev3 boards shipped in May-June 2010 may have had unreliable
+buttons; see the :ref:`errata page <errata>` for details.  `We're
+happy to replace these for you <http://leaflabs.com/contact>`_\ !
 
-.. _troubleshooting-ide-install:
 
-Installation problems
----------------------
+.. _troubleshooting-ide-install:
 
+=======================
+ Installation problems
+=======================
 
 I don't have root/administrator access!
+---------------------------------------
 
-    There are probably hacks or work-arounds to getting programs
-    uploaded without higher level system permissions.  If you can
-    access USB character devices (ACM or ttyUSB style), you should be
-    able to communicate with the Maple and reprogram using an FTDI
-    converter and the serial bootloader, but we haven't tried.
+There are probably hacks or work-arounds to getting programs uploaded
+without higher level system permissions.  If you can access USB
+character devices (ACM or ttyUSB style), you should be able to
+communicate with the Maple and reprogram using an FTDI converter and
+the serial bootloader, but we haven't tried.
 
-    .. TODO: be more helpful
+.. TODO: be more helpful
 
 [Linux] I don't use udev!
+-------------------------
 
-    There is probably a simple way to get autoconfiguration working
-    with devfs; in the meantime, you could try running the entire IDE
-    as root.
+There is probably a simple way to get autoconfiguration working with
+devfs; in the meantime, you could try running the entire IDE as root.
 
-    .. TODO: be more helpful
+.. TODO: be more helpful
 
 .. _troubleshooting-ide-usage:
 
-IDE problems
-------------
+==============
+ IDE problems
+==============
 
-[Mac OSX] The "Board" and "Serial Port" menu items are missing!
+[Mac OS X] The "Board" and "Serial Port" menu items are missing!
+----------------------------------------------------------------
 
-    Sometimes this happens if you try to compile or upload without
-    having a board selected.  The work-around is to restart the
-    IDE. Mysterious!
+Sometimes this happens if you try to compile or upload without having
+a board selected.  The work-around is to restart the IDE. Mysterious!
 
 .. _troubleshooting-compilation:
 
-Common compiler problems
-------------------------
+==========================
+ Common compiler problems
+==========================
 
 ``NullPointerException``
+------------------------
 
-    A classic! Make sure you have selected a board from the pulldown menu. 
+A classic! Make sure you have selected a board from the pulldown menu. 
 
-    .. TODO: remove when Python version is released
+.. TODO: remove when Python version is released
 
 ``undefined reference to setup()/loop()``
+-----------------------------------------
 
-    Your sketch/program either does not include one of the `setup
-    <setup()>`_ or `loop <loop()>`_ functions, or it was not found by
-    the compiler. Your program must include both ``void setup()`` and
-    ``void loop()`` functions; they don't have to do anything, but
-    they **must** be there.
+Your sketch/program either does not include one of the `setup
+<setup()>`_ or `loop <loop()>`_ functions, or it was not found by the
+compiler. Your program must include both ``void setup()`` and ``void
+loop()`` functions; they don't have to do anything, but they **must**
+be there.
 
-    You can start with an example program (to see one in the IDE,
-    click on File > Examples > Stubs > BareMinimum) to get the basic
-    structure.  See also the :ref:`language <language>` documentation.
+You can start with an example program (to see one in the IDE, click on
+File > Examples > Stubs > BareMinimum) to get the basic structure.
+See also the :ref:`language <language>` documentation.
 
-    This is a common error when your entire sketch is blank. 
+This is a common error when your entire sketch is blank.
 
 ``error: 'Serial' was not declared in this scope``
+--------------------------------------------------
 
-    The classic Arduino has only one USART device and uses the unique
-    name "Serial" to control it. Larger devices like the Arduino Mega
-    and the Maple have multiple USARTS referred to as ``Serial1``,
-    ``Serial2``, etc. You probably want ``Serial2`` on the Maple;
-    that's the one connected to pins D0 and D1. See also the
-    :ref:`USART docs <usart>`.
+The classic Arduino has only one USART device and uses the unique name
+"Serial" to control it. Larger devices like the Arduino Mega and the
+Maple have multiple USARTS referred to as ``Serial1``, ``Serial2``,
+etc. You probably want ``Serial2`` on the Maple; that's the one
+connected to pins D0 and D1. See also the :ref:`USART docs <usart>`.
 
 ``File(s) not found``
+---------------------
 
-    There is an intermittent bug with the temporary directory build
-    system that on occasion will lose many of the ``#include``\ d
-    libmaple files. If you recompile everything, it should be fine.
+There is an intermittent bug with the temporary directory build system
+that on occasion will lose many of the ``#include``\ d libmaple
+files. If you recompile everything, it should be fine.
 
-    .. TODO remove when the Python version is released
+.. TODO remove when the Python version is released
 
 .. _troubleshooting-upload:
 
-Common upload problems
-----------------------
+========================
+ Common upload problems
+========================
 
 My program is too large!
+------------------------
 
-    First, make sure you're using the FLASH target instead of RAM;
-    there is several times more FLASH memory available for user
-    programs.
+First, make sure you're using the FLASH target instead of RAM; there
+is several times more FLASH memory available for user programs.
 
 ``No DFU capable USB device found``
+-----------------------------------
 
-    This probably means you don't have a Maple plugged in or powered on! 
+This probably means you don't have a Maple plugged in or powered on! 
 
 I have multiple Maples installed; how do I know which one will get flashed?
+---------------------------------------------------------------------------
 
-    Because the Maple IDE uses DFU to upload programs, you can't
-    select a particular Maple from the Serial Port menu to upload to a
-    particular board. There's no solution to this problem for now:
-    you'll have to just plug in the Maples one at a time. If this is a
-    real problem let us know and we'll see if we can come up with a
-    better solution.
+Because the Maple IDE uses DFU to upload programs, you can't select a
+particular Maple from the Serial Port menu to upload to a particular
+board. There's no solution to this problem for now: you'll have to
+just plug in the Maples one at a time. If this is a real problem let
+us know and we'll see if we can come up with a better solution.
 
 .. _troubleshooting-shell:
 
-Command-line issues
--------------------
+=====================
+ Command-line issues
+=====================
 
 My flash programs don't seem to stick; they behave like they are RAM!
+---------------------------------------------------------------------
 
-    Make sure you :command:`make clean` when switching between FLASH
-    and RAM targets; :command:`make` isn't smart enough to rebuild
-    everything that needs to be for the new target.
+Make sure you :command:`make clean` when switching between FLASH and
+RAM targets; :command:`make` isn't smart enough to rebuild everything
+that needs to be for the new target.
 
 [Linux] ``cdc_acm 3-1:1.0: no more free acm devices``
+-----------------------------------------------------
 
-    This is a nasty one! It means that all 32 possible CDC_ACM serial
-    devices (:file:`/dev/ttyACM25`, etc.) have been used up.
+This is a nasty one! It means that all 32 possible CDC_ACM serial
+devices (:file:`/dev/ttyACM25`, etc.) have been used up.
 
-    The usual cause is using a serial port monitor and not closing it
-    before restarting the Maple or uploading a new program.  The
-    operating system doesn't like that, and locks up that
-    device. After reset the Maple comes back up as a new device. If
-    you develop heavily and don't restart you'll blow right through
-    all 32 devices.
+The usual cause is using a serial port monitor and not closing it
+before restarting the Maple or uploading a new program.  The operating
+system doesn't like that, and locks up that device. After reset the
+Maple comes back up as a new device. If you develop heavily and don't
+restart you'll blow right through all 32 devices.
 
-    The lazy solution is to always close the monitor before
-    restarting, and if you get this error in :file:`dmesg` after a
-    dfu-util "Not Found" error, restart you machine.
+The lazy solution is to always close the monitor before restarting,
+and if you get this error in :file:`dmesg` after a dfu-util "Not
+Found" error, restart you machine.
 
-    The hacker solution is to restart your cdc_acm kernel module. On
-    Ubuntu 09.10, this goes a little something like::
+The hacker solution is to restart your cdc_acm kernel module. On
+Ubuntu 09.10, this goes a little something like::
 
-      $ sudo rmmod cdc-acm
-      $ sudo insmod /lib/modules/2.6.31-20-generic/kernel/drivers/usb/class/cdc-acm.ko
+  $ sudo rmmod cdc-acm
+  $ sudo insmod /lib/modules/2.6.31-20-generic/kernel/drivers/usb/class/cdc-acm.ko
 
 .. _troubleshooting-tips-tricks:
 
-Tips and Tricks
----------------
+=================
+ Tips and Tricks
+=================
 
 .. _troubleshooting-perpetual-bootloader:
 
-**Perpetual Bootloader Mode**
+Perpetual Bootloader Mode
+-------------------------
 
 In this mode, Maple stays a DFU device and does not jump to user code
 until the next reset.  This is useful for guaranteeing that your Maple
@@ -234,13 +215,13 @@ will be available for reprogramming.
 
 To put your Maple into perpetual bootloader mode:
 
-1. Plug your Maple into the USB port.
+#. Plug your Maple into the USB port.
 
-2. Hit the reset button on your Maple (it's the small button at the
-bottom left, labeled RESET).  Notice that it blinks quickly 6 times,
-then blinks slowly a few more times.
+#. Hit the reset button on your Maple (it's the small button at the
+   bottom left, labeled RESET).  Notice that it blinks quickly 6
+   times, then blinks slowly a few more times.
 
-3. Hit reset again, and this time push and hold the other button
-during the 6 fast blinks (the button is on the top right; it is
-labeled BUT). You can release it once the slow blinks start.
+#. Hit reset again, and this time push and hold the other button
+   during the 6 fast blinks (the button is on the top right; it is
+   labeled BUT). You can release it once the slow blinks start.