docs: updated plugin documentation to match recent changes

docs/cli/create.md

@@ -18,7 +18,7 @@ The `create` command initializes a new Quartz project. It helps you set up your
 
 ## Templates
 
-When you run `quartz create`, you can choose a configuration template that pre-configures Quartz for your use case:
+When you run `quartz create`, you can choose a configuration template that pre-configures Quartz for your use case. The selected template always overwrites `quartz.config.yaml`, even if one already exists. After applying the template, Quartz automatically runs plugin resolution to install any plugins the template requires and remove any that are no longer referenced.
 
 - **Default**: A clean Quartz setup with sensible defaults. Best for starting from scratch.
 - **Obsidian**: Optimized for Obsidian vaults with full Obsidian Flavored Markdown support (wikilinks, callouts, mermaid diagrams, etc.). Automatically sets link resolution to `shortest` and skips the link resolution prompt.
@@ -61,7 +61,7 @@ If you run `npx quartz create` without any arguments, it will guide you through
 2. **Select a strategy**: Choose between `new`, `copy`, or `symlink`.
 3. **Enter base URL**: Provide the URL where your site will be hosted.
 4. **Select link resolution**: Choose how your links are formatted (skipped for Obsidian and TTRPG templates).
-5. **Finish**: Quartz will set up the directory structure and create your configuration.
+5. **Finish**: Quartz will set up the directory structure, create your configuration, and automatically install any plugins referenced in the template.
 
 ## Example: Importing an Obsidian Vault
 

docs/cli/plugin.md

@@ -110,6 +110,9 @@ npx quartz plugin check
 
 Remove installed plugins that are no longer referenced in your `quartz.config.yaml`. This is useful for cleaning up after removing plugin entries from your configuration.
 
+> [!note]
+> The `resolve` command also removes orphaned plugins as part of its synchronization. Use `prune` when you only want to clean up without installing anything new.
+
 ```shell
 npx quartz plugin prune
 ```
@@ -122,7 +125,7 @@ npx quartz plugin prune --dry-run
 
 ### resolve
 
-Install plugins that are listed in your `quartz.config.yaml` but missing from the lockfile. This is the inverse of `prune` — it ensures your installed plugins match your configuration.
+Synchronize your installed plugins with your `quartz.config.yaml`. This installs plugins that are in your config but missing from the lockfile, and removes plugins that are in the lockfile but no longer referenced in your config.
 
 ```shell
 npx quartz plugin resolve
@@ -170,7 +173,7 @@ npx quartz plugin prune            # remove orphaned plugins
 
 ### Setting Up from Config
 
-When setting up on a new machine or in CI, resolve any plugins referenced in your config that aren't yet installed:
+When setting up on a new machine or in CI, resolve ensures your installed plugins match your config — installing missing plugins and removing any that are no longer referenced:
 
 ```shell
 npx quartz plugin resolve

docs/cli/upgrade.md

@@ -25,7 +25,9 @@ When you run `npx quartz upgrade`, Quartz performs the following steps:
 
 Because Quartz allows you to customize almost every part of the code, upgrades can sometimes result in merge conflicts. This happens if you have modified a file that the Quartz team has also updated.
 
-If a conflict occurs:
+Quartz automatically handles merge conflicts in `quartz.lock.json` by backing up your lockfile before pulling and restoring it afterward. This prevents the most common source of conflicts during upgrades.
+
+For other files, if a conflict occurs:
 
 1. Git will mark the conflicting sections in the affected files.
 2. You will need to open these files and manually choose which changes to keep.