Reorganize orphaned files from additional-details/ and javascript/

Moved to existing categories (7 files):
- manual-installation-overview.md → advanced-topics/
- render-functions.md → core-concepts/
- server-rendering-tips.md → deployment/
- credits.md → misc/
- asset-pipeline.md → misc/ (warning guide)
- api/README.md → api-reference/README.md
- troubleshooting/README.md → deployment/troubleshooting.md

Moved to outdated/ (4 files):
- tips-for-usage-with-sp6.md (Shakapacker 6 legacy)
- upgrade-webpacker-v3-to-v4.md (explicitly outdated)
- converting-from-custom-webpack-config-to-rails-webpacker-config.md (webpacker legacy)
- webpack.md (outdated Webpack v2 content)

Merged and deleted (1 file):
- node-dependencies-and-npm.md merged into updating-dependencies.md
  (combined yarn upgrade, yarn add, and ncu workflows)

All orphaned files from Steps 1-8 now have homes!

Author: ihabadham

docs/additional-details/manual-installation-overview.md renamed to docs/advanced-topics/manual-installation-overview.md

@@ -10,11 +10,25 @@ Delete any unwanted version constraints from your Gemfile and run:
 bundle update
 ```
 
-## NPM
+## Node/Yarn
+
+### Checking for Outdated Packages
+
+Check for outdated versions of packages:
+
+```bash
+cd client
+yarn outdated
+```
+
+Read CHANGELOGs of major updated packages before you update. You might not be ready for some updates.
+
+### Updating All Dependencies
+
+**Option 1: Using npm-check-updates (Recommended)**
 
 1. Install [npm-check-updates](https://www.npmjs.com/package/npm-check-updates)
-1. Run `yarn outdated` and read CHANGELOGs of major updated packages before you update. You might not be ready for some updates.
-1. Run these commands. You may or may not need to `rm -rf` your `node_modules` directory.
+2. Run these commands. You may or may not need to `rm -rf` your `node_modules` directory.
 
    ```bash
    cd client
@@ -24,8 +38,38 @@ bundle update
 
 Some combinations that I often run:
 
-- remove old installed `node_modules` so you only get what corresponds to `package.json`:
+- Remove old installed `node_modules` so you only get what corresponds to `package.json`:
 
   ```bash
   ncu -u -a && rm -rf node_modules && yarn
   ```
+
+**Option 2: Using yarn upgrade**
+
+To update all dependencies:
+
+```bash
+cd client
+yarn upgrade
+```
+
+To upgrade a specific package:
+
+```bash
+yarn upgrade [package]
+```
+
+### Adding New Dependencies
+
+Typically, you can add your Node dependencies as you normally would:
+
+```bash
+cd client
+yarn add module_name@version
+# or for dev dependencies
+yarn add --dev module_name@version
+```
+
+### Verify After Updates
+
+Confirm that the hot replacement dev server and the Rails server both work after updating dependencies.