Revert package/ restructure, restore scripts to repo root

Moves all automated scripts back to the repo root where setup.sh
expects them. standalone/ remains for manual-run tools.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

README.md

@@ -96,14 +96,14 @@ Then clone and run setup:
 ```bash
 git clone http://100.120.125.113:3000/pdm/security-tools.git
 cd security-tools
-bash package/setup.sh
+bash setup.sh
 ```
 
 **Without Tailscale:**
 ```bash
 git clone https://gitea.pdmarf.co.uk/pdm/security-tools.git
 cd security-tools
-bash package/setup.sh
+bash setup.sh
 ```
 
 To clone to a specific path:
@@ -114,7 +114,7 @@ git clone http://100.120.125.113:3000/pdm/security-tools.git /path/to/destinatio
 
 ## Activating on a New VM
 
-After cloning, run `package/setup.sh` once. It will:
+After cloning, run `setup.sh` once. It will:
 - Ask for your Telegram bot token and chat ID
 - Register cron jobs to run scans daily at 08:00
 - Send a test Telegram message confirming the VM is active
@@ -127,7 +127,7 @@ When changes are pushed to this repo, update any VM by running:
 ```bash
 cd ~/security-tools
 git pull
-bash package/setup.sh
+bash setup.sh
 ```
 
 `setup.sh` is safe to re-run — it skips steps already completed.