incoming cross-references; move api-reference -> reference for cleaner URL

Author: ecormany

docs/absorbance-plate-reader/docs/data.md

@@ -9,4 +9,4 @@ Plate reader data is available on the Recent Protocol Runs screen in the Opentro
 ![CSV data file location](images/csv-data.png){width="90%"} <!-- 100% seems huge -->
 </figure>
 
-You can also use plate reader data immediately in a Python protocol. See the [Python Protocol API documentation](https://docs.opentrons.com/v2/modules/absorbance_plate_reader.html#using-plate-reader-data) for more information.
+You can also use plate reader data immediately in a Python protocol. See the [Python Protocol API documentation](../python-api/modules/absorbance-plate-reader.md#using-plate-reader-data) for more information.

docs/flex/docs/additional-docs.md

@@ -18,7 +18,7 @@ The [Opentrons Knowledge Hub](https://opentrons.com/resources/knowledge-hub/) ho
 
 ## Python Protocol API documentation
 
-The [online documentation for the Opentrons Python Protocol API](https://docs.opentrons.com/v2/) describes how to write automated biology lab protocols for Opentrons robots and hardware modules. The documentation includes a [Tutorial](https://docs.opentrons.com/v2/tutorial.html) for users writing their first Python protocol.
+The [documentation for the Opentrons Python Protocol API](../python-api/index.md) describes how to write automated biology lab protocols for Opentrons robots and hardware modules. The documentation includes a [Tutorial](../python-api/tutorial.md) for users writing their first Python protocol.
 
 The Python API documentation covers writing Python code to:
 
@@ -34,7 +34,7 @@ The Python API documentation covers writing Python code to:
 
 - Move instruments to exact locations in the working area.
 
-There is also a [Python API reference](https://docs.opentrons.com/v2/new_protocol_api.html) with information about all of the classes and methods that comprise the API.
+There is also a [Python API reference](../python-api/reference/protocols.md) with information about all of the classes and methods that comprise the API.
 
 ## Opentrons HTTP API reference
 

docs/flex/docs/advanced-operation/command-line.md

@@ -4,7 +4,7 @@ title: "Opentrons Flex: Command Line Operation Over SSH"
 
 Opentrons Flex gives you command-line access to its operating system through a Secure Shell (SSH) terminal connection. Terminal access lets you:
 
-- Run protocols directly via the [Python API and command line](https://docs.opentrons.com/v2/advanced_control/command_line.html#command-line).
+- Run protocols directly via the [Python API and command line](../../python-api/advanced-control/command-line.md).
 - Perform advanced tasks like customizing the robot's Python environment.
 - Execute protocols that reference external files on disk (apart from custom labware definition files).
 

docs/flex/docs/advanced-operation/jupyter-notebook.md

@@ -11,4 +11,4 @@ Access your robot's Jupyter Notebook either:
 - In your web browser. Navigate directly to `http://<robot-ip>:48888`, replacing `<robot-ip>` with the local IP address of your Flex.
 
 For more details on using Jupyter, including preparing executable cells
-of code and running them on a robot, see the [Jupyter Notebook section](https://docs.opentrons.com/v2/advanced_control/jupyter.html#jupyter-notebook) of the Python Protocol API documentation.
+of code and running them on a robot, see the [Jupyter Notebook section](../../python-api/advanced-control/jupyter.md) of the Python Protocol API documentation.

docs/flex/docs/glossary.md

@@ -244,7 +244,7 @@ A protocol script written using the Opentrons *Python Protocol API*. See the [Wr
 
 ##### Python Protocol API
 
-A Python package that exposes a wide range of liquid handling features on Opentrons robots. See the [Python Protocol API section](protocols/python-api.md) in the Protocol Development chapter and the online [Opentrons Python Protocol API documentation](https://docs.opentrons.com/v2/).
+A Python package that exposes a wide range of liquid handling features on Opentrons robots. See the [Python Protocol API section](protocols/python-api.md) in the Protocol Development chapter and the [Opentrons Python Protocol API documentation](../python-api/index.md).
 
 ##### Removable deck slot
 

docs/flex/docs/introduction.md

@@ -19,7 +19,7 @@ Opentrons Flex includes advanced features to help you automate any workflow, ava
 | **Module caddies** | Flex modules fit into caddies that occupy space below the deck. Caddies place your labware closer to the deck surface and allow for below-deck cable routing. Caddies enable even more module and labware configurations on the deck. |
 | **Moveable trash** | The trash bin can go in multiple deck locations on Flex. The default location (slot A3) is the recommended position. You can also use the gripper to dispose of trash in the optional waste chute. |
 | **Liquid detection** | Pressure sensors in Flex pipettes detect liquid in wells, including tip contact and liquid level. This feature lets you control the Flex's pipetting relative to a liquid meniscus, and alerts you if wells are empty. |
-| **Liquid classes** | Use [liquid class settings](https://docs.opentrons.com/v2/liquid_classes.html) to optimize Flex's pipetting behavior for your liquids, including fine-tuned control of pipette actions like flow rate and submerge speed. You can easily apply Opentrons-verified settings for aqueous, viscous, or volatile liquids using Python commands, in a quick transfer, or in Protocol Designer. |
+| **Liquid classes** | Use [liquid class settings](../python-api/liquid-classes.md) to optimize Flex's pipetting behavior for your liquids, including fine-tuned control of pipette actions like flow rate and submerge speed. You can easily apply Opentrons-verified settings for aqueous, viscous, or volatile liquids using Python commands, in a quick transfer, or in Protocol Designer. |
 
 ## Flex and OT-2 
 

docs/flex/docs/modules/heater-shaker.md

@@ -71,7 +71,7 @@ You can purchase adapters directly from Opentrons:
 
 ### Software control
 
-The Heater-Shaker is fully programmable in Protocol Designer and the Python Protocol API. The Python API additionally allows for other protocol steps to be performed in parallel while the Heater-Shaker is active. See [Non-blocking commands](https://docs.opentrons.com/v2/modules/heater_shaker.html#non-blocking-commands) in the API documentation for details on adding parallel steps to your protocols.
+The Heater-Shaker is fully programmable in Protocol Designer and the Python Protocol API. The Python API additionally allows for other protocol steps to be performed in parallel while the Heater-Shaker is active. See [Non-blocking commands](../../python-api/modules/heater-shaker.md#non-blocking-commands) in the API documentation for details on adding parallel steps to your protocols.
 
 Outside of protocols, the Opentrons App can display the current status of the Heater-Shaker and can directly control the heater, shaker, and labware latch.
 

docs/flex/docs/modules/index.md

@@ -9,7 +9,7 @@ This chapter summarizes the functions and physical specifications of modules tha
 !!! tip
     - For complete instructions on module installation and use, refer to the quickstart guide that shipped with your unit or find its manual in the [Modules category](../../modules/index.md) of the Opentrons Documentation website.
 
-    - For details on integrating modules into your protocols, see the [Protocol Designer section](../protocols/designer.md) of the Protocol Development chapter or the [Hardware Modules section](https://docs.opentrons.com/v2/new_modules.html) of our Python API documentation.
+    - For details on integrating modules into your protocols, see the [Protocol Designer section](../protocols/designer.md) of the Protocol Development chapter or the [Hardware Modules section](../../python-api/modules/index.md) of our Python API documentation.
 
 
 ## Supported modules

docs/flex/docs/protocols/python-api.md

@@ -5,7 +5,7 @@ title: "Opentrons Flex: Python Protocol API"
 Writing protocol scripts in Python gives you the most fine-grained control of Opentrons Flex. Version 2 of the Python Protocol API is a single Python package that exposes a wide range of liquid handling features on Opentrons robots. 
 
 !!! info "Additional Documentation"
-    For an idea of the breadth of the API, check out the [full online documentation](https://docs.opentrons.com/v2/), which includes topic-based articles as well as a [comprehensive reference](https://docs.opentrons.com/v2/new_protocol_api.html) of all methods and functions contained in the package. If you've never written an Opentrons protocol before and want to build one from scratch, follow the [Tutorial](https://docs.opentrons.com/v2/tutorial.html).
+    For an idea of the breadth of the API, check out the [full API documentation](../../python-api/index.md), which includes topic-based articles as well as a [comprehensive reference](../../python-api/reference/protocols.md) of all methods and functions contained in the package. If you've never written an Opentrons protocol before and want to build one from scratch, follow the [Tutorial](../../python-api/tutorial.md).
 
 ## Writing and running scripts
 
@@ -17,14 +17,14 @@ Python protocols generally follow the same basic structure:
 
 3.  Defining a `run()` function that contains all of the instructions to the robot, including:
 
-    - [Pipettes](https://docs.opentrons.com/v2/new_pipette.html) the protocol will use.
+    - [Pipettes](../../python-api/pipettes/index.md) the protocol will use.
 
-    - Locations of [modules](https://docs.opentrons.com/v2/new_modules.html), [labware](https://docs.opentrons.com/v2/new_labware.html), and [deck fixtures](https://docs.opentrons.com/v2/deck_slots.html#deck-configuration).
+    - Locations of [modules](../../python-api/modules/index.md), [labware](../../python-api/labware.md), and [deck fixtures](../../python-api/deck-slots.md#deck-configuration).
 
-    - Liquid [classes](https://docs.opentrons.com/v2/liquid_classes) or [types and locations](https://docs.opentrons.com/v2/new_labware.html#labeling-liquids-in-labware) (optional).
+    - Liquid [classes](../../python-api/liquid-classes.md) or [types and locations](../../python-api/labware.md#labeling-liquids-in-labware) (optional).
 
-    - Commands the system will physically execute (e.g., [simple](https://docs.opentrons.com/v2/new_atomic_commands.html) or [complex](https://docs.opentrons.com/v2/new_complex_commands.html) liquid
-      handling commands, [module](https://docs.opentrons.com/v2/new_modules.html) commands, or [movement](https://docs.opentrons.com/v2/robot_position.html) commands).
+    - Commands the system will physically execute (e.g., [simple](../../python-api/building-block-commands/index.md) or [complex](../../python-api/complex-commands/index.md) liquid
+    handling commands, [module](../../python-api/modules/index.md) commands, or [movement](../../python-api/robot-position.md) commands).
 
 ```python
 from opentrons import protocol_api
@@ -77,21 +77,21 @@ Certain configurations allow changing which nozzles are used. For example, you c
 
 Starting in API version 2.18, you can define user-customizable variables in your Python protocols. This gives you greater flexibility and puts extra control in the hands of the technician running the protocol — without forcing them to switch between lots of protocol files or write code themselves.
 
-Runtime parameters can customize Boolean, numerical, and string values in your protocol. And starting in API version 2.20, you can require a CSV file of data to be parsed and used in the protocol. See the [API documentation on runtime parameters](https://docs.opentrons.com/v2/runtime_parameters.html) for information on writing them into protocols, and see the [Runtime Parameters section](../touchscreen/protocol-setup.md#runtime-parameters) of the Touchscreen chapter for information on changing parameter values during run setup.
+Runtime parameters can customize Boolean, numerical, and string values in your protocol. And starting in API version 2.20, you can require a CSV file of data to be parsed and used in the protocol. See the [API documentation on runtime parameters](../../python-api/runtime-parameters/index.md) for information on writing them into protocols, and see the [Runtime Parameters section](../touchscreen/protocol-setup.md#runtime-parameters) of the Touchscreen chapter for information on changing parameter values during run setup.
 
 ### Robot motor control 
 
-Starting in API version 2.22, you can move individual robot motors like the gantry, pipette plunger, and gripper jaws with [robot motor control commands](https://docs.opentrons.com/v2/advanced_control/motor_control.html#motor-control). Use helper and movement commands to calculate and move robot axes to precise positions on the Flex deck, and gripper commands to open or close the Flex Gripper jaws. 
+Starting in API version 2.22, you can move individual robot motors like the gantry, pipette plunger, and gripper jaws with [robot motor control commands](../../python-api/advanced-control/robot-motors.md). Use helper and movement commands to calculate and move robot axes to precise positions on the Flex deck, and gripper commands to open or close the Flex Gripper jaws. 
 
 Unlike other protocol commands, robot motor control commands execute movements independent of labware and hardware positions on the Flex. This lets you complete advanced tasks, like using 3D-printed labware in your protocols, moving the Flex's z-axis carriage without a pipette attached, or simultaneously pipetting and holding labware with the Flex Gripper. 
 
 ###  Liquid level detection 
 
-Sensors in Flex pipettes can detect the level of liquid in a well. You can use this feature to target a [liquid meniscus](https://docs.opentrons.com/v2/robot_position.html?highlight=liquid+level#meniscus) while aspirating, dispensing, or mixing in a Python protocol. 
+Sensors in Flex pipettes can detect the level of liquid in a well. You can use this feature to target a [liquid meniscus](../../python-api/robot-position.md#meniscus) while aspirating, dispensing, or mixing in a Python protocol. 
 
 ### Non-blocking commands
 
-Some module commands that take a long time to complete (such as heating from ambient temperature to a high temperature) can be run in a *non-blocking* manner. This lets your protocol save time by continuing on to other pipetting tasks instead of waiting for the command to complete. Non-blocking commands are currently supported on the [Heater-Shaker Module](https://docs.opentrons.com/v2/modules/heater_shaker.html#non-blocking-commands).
+Some module commands that take a long time to complete (such as heating from ambient temperature to a high temperature) can be run in a *non-blocking* manner. This lets your protocol save time by continuing on to other pipetting tasks instead of waiting for the command to complete. Non-blocking commands are currently supported on the [Heater-Shaker Module](../../python-api/modules/heater-shaker.md#non-blocking-commands).
 
 ### Python packages
 

docs/flex/docs/touchscreen/protocol-details.md

@@ -29,7 +29,7 @@ The Summary tab shows:
 The Parameters tab lists all of the runtime parameters that you can configure from the touchscreen while setting up the protocol. The Default Value column shows the value that the protocol will use if you don't change it. The Range column shows the maximum and minimum, list of choices, or number of choices depending on the parameter type.
 
 !!! note
-    Runtime parameters are only available in Python protocols that define their names, descriptions, and possible values. See [Runtime Parameters](https://docs.opentrons.com/v2/runtime_parameters.html) in the Python API documentation for information on defining parameters and using their values. JSON protocols do not currently support this feature.
+    Runtime parameters are only available in Python protocols that define their names, descriptions, and possible values. See [Runtime Parameters](../../python-api/runtime-parameters/index.md) in the Python API documentation for information on defining parameters and using their values. JSON protocols do not currently support this feature.
 
 ## Hardware tab