Fix broken doc links and resolve dependency conflicts (project-chip#37694)

* Fix broken doc links and resolve dependency conflicts

* Fix MyST cross-reference error in vs_code_development.md

* Restyled by prettier-markdown

* Delete docs/examples/chef/README_DEVICE.md

* Delete docs/examples/chef/README_OTCLI.md

* Delete docs/examples/chef/README_SHELL.md

---------

Co-authored-by: Restyled.io <commits@restyled.io>

Author: 2 people

docs/development_controllers/chip-repl/index.md

@@ -9,7 +9,7 @@
 ```
 
 -   [Matter REPL](./matter-repl.md)
--   [Intro](./Matter_REPL_Intro.ipynb)
--   [Access Control](./Matter_Access_Control.ipynb)
--   [Basic interactions](./Matter_Basic_Interactions.ipynb)
--   [Fabric Commissioning](./Matter_Multi_Fabric_Commissioning.ipynb)
+-   [Intro](https://github.com/project-chip/connectedhomeip/blob/master/docs/development_controllers/chip-repl/Matter_REPL_Intro.ipynb)
+-   [Basic interactions](https://github.com/project-chip/connectedhomeip/blob/master/docs/development_controllers/chip-repl/Matter_Basic_Interactions.ipynb)
+-   [Access Control](https://github.com/project-chip/connectedhomeip/blob/master/docs/development_controllers/chip-repl/Matter_Access_Control.ipynb)
+-   [Multi Fabric Commissioning](https://github.com/project-chip/connectedhomeip/blob/master/docs/development_controllers/chip-repl/Matter_Multi_Fabric_Commissioning.ipynb)

docs/development_controllers/index.md

@@ -9,5 +9,5 @@ chip-repl/index
 chip-tool/index
 ```
 
--   [chip-tool](./chip-tool)
--   [chip-repl](./chip-repl)
+-   [chip-tool](./chip-tool/index.md)
+-   [chip-repl](./chip-repl/index.md)

docs/platforms/esp32/vs_code_development.md

@@ -18,7 +18,9 @@ Follow
 [these](https://github.com/project-chip/connectedhomeip/edit/master/docs/VSCODE_DEVELOPMENT.md)
 steps to set up Visual Studio Code for Matter development.
 
-### Linux <a name="linux">
+(linux)=
+
+### Linux
 
 For Espressif esp32 devices:
 
@@ -68,4 +70,4 @@ For Espressif esp32 devices:
 
 1. Open connectedhomeip within WSL on Visual Studio Code.
 
-1. Perform step 2 onwards from [Linux](#linux) guide.
+1. Perform step 2 onwards from {ref}`linux` guide.

docs/requirements.txt

@@ -1,6 +1,6 @@
-docutils==0.17.1
-Sphinx>=4.5
+docutils==0.21.2
+Sphinx==8.2.0
 sphinx-book-theme
-myst-parser
+myst-parser>=2.0.0
 breathe>=4.34
-pydata-sphinx-theme==0.14.4
+pydata-sphinx-theme==0.16.1

examples/energy-management-app/linux/README.md

@@ -241,7 +241,7 @@ data (e.g. fabric info).
 
 -   See chip-repl documentation in:
     -   [Working with Python CHIP Controller](../../../docs/development_controllers/chip-repl/python_chip_controller_building.md)
-    -   [Matter_REPL_Intro](../../../docs/development_controllers/chip-repl/Matter_REPL_Intro.ipynb)
+    -   [Matter_REPL_Intro](https://github.com/project-chip/connectedhomeip/blob/master/docs/development_controllers/chip-repl/Matter_REPL_Intro.ipynb)
 
 ### Building chip-repl: