change to use mermaid in protocols docs

Author: taichunmin

Home.md

@@ -6,32 +6,32 @@ This Guide is split up into multiple "subguides":
 
 ### About the device
 
-- [[Whitepaper|technical_whitepaper]]: Discover what the Chameleon Ultra is capable of.
+- [Whitepaper](./technical_whitepaper.md): Discover what the Chameleon Ultra is capable of.
 
-- [[Hardware|hardware]]: Learn to know the hardware of your Chameleon.
+- [Hardware](./hardware.md): Learn to know the hardware of your Chameleon.
 
-- [[Firmware|firmware]]: Your Chameleon runs a firmware, learn what it can do and how to use it.
+- [Firmware](./firmware.md): Your Chameleon runs a firmware, learn what it can do and how to use it.
 
 ### Interacting with the device
 
-- [[Quickstart|quickstart]]: For the impatient people to just get you up and running with anything.
+- [Quickstart](./quickstart.md): For the impatient people to just get you up and running with anything.
 
-- [[CLI|cli]]: The official way to control your Chameleon is via the **C**ommand **L**ine **I**nterface (CLI). Learn how to install and master the CLI.
+- [CLI](./cli.md): The official way to control your Chameleon is via the **C**ommand **L**ine **I**nterface (CLI). Learn how to install and master the CLI.
 
-- [[GUIs|gui]]: Some people also develop **G**raphical **U**ser **I**nterfaces (GUIs), these may be a good start for people that do not want to deal with a CLI.
+- [GUIs](./gui.md): Some people also develop **G**raphical **U**ser **I**nterfaces (GUIs), these may be a good start for people that do not want to deal with a CLI.
 
-- [[Troubleshooting|troubleshooting]]: For when things go wrong, here are some common tips to maybe fix whatever issue you might have.
+- [Troubleshooting](./troubleshooting.md): For when things go wrong, here are some common tips to maybe fix whatever issue you might have.
 
 ### For developers
 
-- [[Development|development]]: For all developers. This covers how to build firmware from source and set up a development environment.
+- [Development](./development.md): For all developers. This covers how to build firmware from source and set up a development environment.
 
-- [[SDKs|sdk]]: SDKs for Chameleon, useful if you want to develop your own application to control Chameleon.
+- [SDKs](./sdk.md): SDKs for Chameleon, useful if you want to develop your own application to control Chameleon.
 
-- [[Protocol|protocol]]: The gory details of the communication protocol, useful if you want to develop your own client.
+- [Protocol](./protocol/README.md): The gory details of the communication protocol, useful if you want to develop your own client.
 
 ### Miscellaneous 
 
-- [[Modding|modding]]: Third party moddings worth mentioning.
+- [Modding](./modding.md): Third party moddings worth mentioning.
 
-- [[FAQ|faq]]: **F**requently **A**sked **Q**uestions, if you have a question, it might already be answered here.
+- [FAQ](./faq.md): **F**requently **A**sked **Q**uestions, if you have a question, it might already be answered here.

chameleonultragui.md

@@ -65,7 +65,7 @@ The *Mifare Classic emulator settings* section allows you to toggle various beha
 - *Gen2 Magic Mode*: behaves like a gen2 magic card, makes Block 0 writable ;
 - *Use UID/SAK/ATQA from 0 block*: the Chameleon Ultra stores the UID and other anti-collision data independently of the card content. Enabling this setting tells the Chameleon to derive them from card content block 0. Only for MFC with 4-byte UID ;
 - *Collect nonces (Mfkey32)*: it toggles nonce collection for mfkey32. When enabled you will be prompted to present the Chameleon to a reader. After you have collected nonces the *Present Chameleon to reader* message will change into a *Recover Keys from x nonces* button. Pressing this will start the recovery process ;
-- *Write mode*: Please refer to the [[firmware docs|firmware]].
+- *Write mode*: Please refer to the [firmware docs](./firmware.md).
 
 ### Search dialog
 ![Search Dialog](./images/cugui-searchdialog.png)

firmware.md

@@ -2,7 +2,7 @@
 
 The Chameleon flash contains several parts: the bootloader and its settings, the application, the user data and the SoftDevice.
 
-NOTE: If you are a developer searching for the building instructions, look into [[development|development]]
+NOTE: If you are a developer searching for the building instructions, look into [development](./development.md).
 
 ## The Bootloader
 

gui.md

@@ -3,6 +3,6 @@
 There are multiple GUIs to control your Chameleon, two are featured in this documentation.
 Note that in spite of what their name may suggest, all GUIs support both the Ultra and the Lite.
 
-- [[Chameleon Ultra GUI|chameleonultragui]] ([github](https://github.com/GameTec-live/ChameleonUltraGUI))
+- [Chameleon Ultra GUI](./chameleonultragui.md) ([github](https://github.com/GameTec-live/ChameleonUltraGUI))
 
 - [MTools Lite for iOS](https://shop.mtoolstec.com/mifare-classic-tool-for-ios)