docs: restructure documentation

docs/manual/configuring/custom-plugins.md

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+# Custom Plugins {#ch-custom-plugins}
+
+Neovim-flake, by default, exposes a wide variety of plugins as module options
+for your convience and bundles necessary dependencies into neovim-flake's
+runtime. In case a plugin is not available in neovim-flake, you may consider
+making a pull request to neovim-flake to include it as a module or you may add
+it to your configuration locally.
+
+## Adding Plugins {#ch-adding-plugins}
+
+There are multiple way of adding custom plugins to your neovim-flake
+configuration.
+
+You can use custom plugins, before they are implemented in the flake. To add a
+plugin, you need to add it to your config's `vim.startPlugins` array.
+
+Adding a plugin to `startPlugins` will not allow you to configure the plugin
+that you have addeed, but neovim-flake provides multiple way of configuring any
+custom plugins that you might have added to your configuration.
+
+```{=include=} sections
+custom-plugins/configuring.md
+custom-plugins/new-method.md
+custom-plugins/old-method.md
+```