feat: reorganise bash scripts and add comprehensive documentation (#6)

## Summary

This PR completes the bash script restructuring and adds comprehensive documentation across all script categories.

### Bash Restructuring

- Moved cohort shell scripts (`remove_github_members.sh`, `update_github_teams.sh`) from `python/cohort/` into a new `bash/cohort/` directory
- Moved existing bash utilities (`add-keys-to-git.sh`, `fix-yubikey-perms.sh`, `list-yubikey-ssh-keys.sh`) into a new `bash/yubikey/` subdirectory
- Updated `run.sh` to support **Bash** as a third language option alongside TypeScript and Python
  - Bash scripts are run directly (no 1Password secret injection needed)
  - Category discovery and script listing works the same as for TS/Python
  - Removed dead "Root Scripts" logic that was no longer needed

### Documentation

Added `README.md` files for all script categories that were missing them:

- `bash/cohort/README.md` — cohort GitHub team management scripts
- `bash/yubikey/README.md` — YubiKey SSH key and permission utilities
- `typescript/src/crowdin/README.md` — Crowdin translation management scripts
- `typescript/src/discord/README.md` — Discord bot utility scripts
- `typescript/src/discourse/README.md` — Discourse forum management scripts
- `typescript/src/gitea/README.md` — Gitea bulk repository operation scripts
- `typescript/src/github/README.md` — GitHub API interaction scripts
- `typescript/src/music/README.md` — Music file metadata tools
- `typescript/src/s3/README.md` — S3-compatible object storage scripts
- `typescript/src/security/README.md` — Security analysis and reporting scripts
- `python/cohort/README.md` — Updated to remove moved shell scripts, fix usage commands

Also updated project-level docs:

- **`README.md`** — Corrected project structure, fixed running instructions (removed references to non-existent `make run-ts`/`make run-py` targets), added Bash prerequisites
- **`CLAUDE.md`** — Updated project overview, structure, development standards, and script-adding guides to reflect the current state of the project

✨ This PR was created with help from Hikari~ 🌸

Co-authored-by: Naomi Carrigan <commits@nhcarrigan.com>
Reviewed-on: #6
Co-authored-by: Hikari <hikari@nhcarrigan.com>
Co-committed-by: Hikari <hikari@nhcarrigan.com>

python/cohort/send_checkin.py

@@ -0,0 +1,97 @@
+"""Send biweekly check-in messages to all team Discord channels.
+
+Posts a check-in prompt to each team channel and automatically creates a thread
+for responses. Members who do not respond by the deadline may be removed for
+inactivity.
+
+Data files (place in data/):
+  - team_message_ids.json  Channel IDs per team (generated by send_team_messages.py)
+
+Env vars:
+  - DISCORD_BOT_TOKEN  Bot token for the Discord API
+"""
+
+import asyncio
+import json
+import os
+from pathlib import Path
+
+import aiohttp
+
+DATA_DIR = Path(__file__).parent.parent.parent / "data"
+
+DISCORD_BOT_TOKEN = os.environ["DISCORD_BOT_TOKEN"]
+DISCORD_API = "https://discord.com/api/v10"
+GUILD_ID = "692816967895220344"
+
+CHECK_IN_MESSAGE = """@everyone it is time for Naomi to do a check in. I need **each and every one of you** to respond to this message **in the thread** by Monday, or you **will be removed** for inactivity.
+
+1. What have you achieved over the last two weeks?
+2. What is your focus for the next two weeks?
+3. How much time can you **reliably** commit to your team over the next two weeks?
+4. Are you facing any **blockers** or **challenges** that are preventing you from contributing?
+5. Do you need **help** from your team leaders or from Naomi to get unstuck?
+"""
+
+
+async def send_checkin_to_teams() -> None:
+    """Send check-in message to all team channels (except Jade Jasmine)."""
+    with open(DATA_DIR / "team_message_ids.json") as f:
+        team_data = json.load(f)
+
+    headers = {
+        "Authorization": f"Bot {DISCORD_BOT_TOKEN}",
+        "Content-Type": "application/json",
+    }
+
+    async with aiohttp.ClientSession() as session:
+        for team_name, data in team_data.items():
+            if team_name == "jade-jasmine":
+                print(f"⏭️  Skipping {team_name} (dissolved)")
+                continue
+
+            channel_id = data["channel_id"]
+            print(f"📤 Sending check-in to {team_name} (channel {channel_id})...")
+
+            async with session.post(
+                f"{DISCORD_API}/channels/{channel_id}/messages",
+                headers=headers,
+                json={"content": CHECK_IN_MESSAGE},
+            ) as resp:
+                if resp.status == 200:
+                    message_data = await resp.json()
+                    message_id = message_data["id"]
+                    print(f"   ✅ Message sent! Message ID: {message_id}")
+
+                    thread_name = (
+                        f"Check-in Responses - {team_name.replace('-', ' ').title()}"
+                    )
+                    async with session.post(
+                        f"{DISCORD_API}/channels/{channel_id}/messages/{message_id}/threads",
+                        headers=headers,
+                        json={
+                            "name": thread_name,
+                            "auto_archive_duration": 10080,
+                        },
+                    ) as thread_resp:
+                        if thread_resp.status == 201:
+                            thread_data = await thread_resp.json()
+                            thread_id = thread_data["id"]
+                            print(f"   🧵 Thread created! Thread ID: {thread_id}")
+                        else:
+                            error_text = await thread_resp.text()
+                            print(
+                                f"   ❌ Failed to create thread: "
+                                f"{thread_resp.status} - {error_text}"
+                            )
+                else:
+                    error_text = await resp.text()
+                    print(f"   ❌ Failed to send message: {resp.status} - {error_text}")
+
+            await asyncio.sleep(1)
+
+    print("\n✅ Check-in messages sent to all teams!")
+
+
+if __name__ == "__main__":
+    asyncio.run(send_checkin_to_teams())