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/add_github_team_members.py

@@ -1,15 +1,29 @@
 #!/usr/bin/env python3
-"""Add GitHub users to their appropriate teams in nhcarrigan-spring-2026-cohort org"""
+"""Add GitHub users to their appropriate teams in the cohort GitHub organisation.
+
+Uses the GitHub CLI to add each member to their corresponding team and, for
+leaders, to the team's leaders sub-team.
+
+Data files (place in data/):
+  - team_assignments.json   Team rosters with leaders and participants per team
+  - discord_to_github.json  Mapping of Discord IDs to GitHub usernames
+
+Env vars:
+  - None (uses `gh` CLI for authentication)
+"""
 
 import json
 import subprocess
 import time
+from pathlib import Path
+
+DATA_DIR = Path(__file__).parent.parent.parent / "data"
 
 # Load team assignments and Discord to GitHub mappings
-with open("team_assignments.json") as f:
+with open(DATA_DIR / "team_assignments.json") as f:
     teams = json.load(f)
 
-with open("discord_to_github.json") as f:
+with open(DATA_DIR / "discord_to_github.json") as f:
     discord_to_github = json.load(f)
 
 # Map team names to GitHub team slugs