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_team_checkin.py

@@ -0,0 +1,104 @@
+#!/usr/bin/env python3
+"""Send a capacity check-in message to each team channel.
+
+Posts a message asking whether the team feels able to complete their project
+given their current member count, and invites them to request support if needed.
+
+Data files (place in data/):
+  - team_message_ids.json   Channel and role IDs per team (from send_team_messages.py)
+  - team_assignments.json   Team rosters used to report current member counts
+
+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"]
+NAOMI_ID = "465650873650118659"
+
+
+def build_checkin_message(team_name: str, team: dict, role_id: str) -> str:
+    """Build the team check-in message."""
+    total_members = len(team["leaders"]) + len(team["participants"])
+    num_leaders = len(team["leaders"])
+    num_participants = len(team["participants"])
+
+    leader_text = "leader" if num_leaders == 1 else "leaders"
+    participant_text = "participant" if num_participants == 1 else "participants"
+
+    return f"""## Team Check-In
+
+Your team currently has **{total_members} members** ({num_leaders} {leader_text} + {num_participants} {participant_text}).
+
+Given the recent changes to team size, we want to make sure you feel confident moving forward with your project. Please discuss as a team and let us know:
+
+**Do you feel you can still complete your project with your current team size?**
+
+If you have concerns about capacity, need additional support, or would like to discuss options (such as combining with another team or adjusting project scope), please ping <@{NAOMI_ID}> and we'll work together to find a solution.
+
+Your success is the priority here - we want to make sure every team has what they need to build something amazing! 💜
+
+-# <@&{role_id}>"""
+
+
+async def send_message(
+    session: aiohttp.ClientSession, channel_id: str, content: str
+) -> dict | None:
+    """Send a message to a Discord channel."""
+    url = f"https://discord.com/api/v10/channels/{channel_id}/messages"
+    headers = {
+        "Authorization": f"Bot {DISCORD_BOT_TOKEN}",
+        "Content-Type": "application/json",
+    }
+    payload = {"content": content}
+
+    async with session.post(url, headers=headers, json=payload) as resp:
+        if resp.status in [200, 201]:
+            return await resp.json()
+        error_text = await resp.text()
+        print(
+            f"❌ Failed to send message to channel {channel_id}: {resp.status} - {error_text}"  # noqa: E501
+        )
+        return None
+
+
+async def main() -> None:
+    """Send check-in messages to all teams."""
+    with open(DATA_DIR / "team_message_ids.json") as f:
+        team_data = json.load(f)
+
+    with open(DATA_DIR / "team_assignments.json") as f:
+        teams = json.load(f)
+
+    async with aiohttp.ClientSession() as session:
+        print("📢 Sending team check-in messages...\n")
+
+        for team in teams:
+            team_name = team["name"]
+            channel_id = team_data[team_name]["channel_id"]
+            role_id = team_data[team_name]["role_id"]
+
+            print(f"Processing {team_name}...")
+
+            checkin_msg = build_checkin_message(team_name, team, role_id)
+            result = await send_message(session, channel_id, checkin_msg)
+
+            if result:
+                total = len(team["leaders"]) + len(team["participants"])
+                print(f"  ✅ Sent check-in ({total} members)")
+
+            await asyncio.sleep(2)
+
+        print("\n✨ Done sending all team check-in messages!")
+
+
+if __name__ == "__main__":
+    asyncio.run(main())