docs: convert remaining prose .rst to MyST .md (pass 2)

Continues the rst→md migration started in PyAutoFit#1245. Converts
the root README and the two `autoarray/config/.../README.rst` files
to MyST. Also:

- pyproject.toml: switches readme content-type to text/markdown
- MANIFEST.in: ships README.md in the sdist
- docs/index.md: replaces the eval-rst include of README.rst with
  the MyST-native `{include}` directive on README.md

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: 2 people

MANIFEST.in

@@ -1,6 +1,6 @@
 # MANIFEST.in
 exclude .gitignore
-include README.rst
+include README.md
 include setup.cfg
 include CITATIONS.rst
 include LICENSE

README.rst README.mdREADME.rst renamed to README.md

@@ -1,2 +1,3 @@
-# PyAutoArray
-A library for manipulating arrays within the PyAuto software framework
+# PyAutoArray
+
+A library for manipulating arrays within the PyAuto software framework

autoarray/config/README.md

@@ -0,0 +1,13 @@
+The `config` folder contains configuration files which customize default **PyAutoLens**.
+
+# Folders
+
+- `priors`: Configs defining default priors assumed on every model component and set of parameters.
+- `visualize`: Configs defining what images are output by a lens model fit.
+
+# Files
+
+- `general.yaml`: Customizes general **PyAutoLens** settings.
+- `grids.yaml`: Customize default behaviour of grids when used for calculations.
+- `logging.yaml`: Customizes the logging behaviour.
+- `notation.yaml`: Configs defining labels and formatting of model parameters when used for visualization.

autoarray/config/README.rst

@@ -0,0 +1,10 @@
+The `config` folder contains configuration files which customize default **PyAutoLens**.
+
+# Files
+
+- `general.yaml`: Customizes general visualization settings (e.g. the matplotlib backend).
+- `include.yaml`: Customize features that appears on plotted images by default (e.g. a mask, a grid).
+- `plots.yaml`: Customize which figures are output during a model-fit.
+- `mat_wrap.yaml`: Specify the default matplotlib settings when figures and subplots are plotted.
+- `mat_wrap_1d.yaml`: Specify the default matplotlib settings when 1D figures and subplots are plotted.
+- `mat_wrap_2d.yaml`: Specify the default matplotlib settings when 2D figures and subplots are plotted.

autoarray/config/visualize/README.md

@@ -1,3 +1,2 @@
-```{eval-rst}
-.. include:: ../README.rst
+```{include} ../README.md
 ```

autoarray/config/visualize/README.rst

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "autoarray"
 dynamic = ["version"]
   description="PyAuto Data Structures"
-readme = { file = "README.rst", content-type = "text/x-rst" }
+readme = { file = "README.md", content-type = "text/markdown" }
 license = { text = "MIT" }
 requires-python = ">=3.9"
 authors = [