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>

bash/yubikey/README.md

@@ -0,0 +1,109 @@
+# YubiKey Scripts
+
+Shell scripts for managing YubiKey hardware security keys on WSL (Windows Subsystem for Linux). Covers SSH key extraction, Git signing key configuration, and fixing USB permission issues that commonly arise in WSL environments.
+
+All scripts require a YubiKey to be attached and forwarded to WSL via `usbipd`. The `ykman` and `yubico-piv-tool` packages must be installed.
+
+## Getting Started
+
+Run scripts via the interactive runner from the project root:
+
+```bash
+make run
+# Select: Bash → yubikey → <script>
+```
+
+Or run directly:
+
+```bash
+bash bash/yubikey/<script-name>.sh
+```
+
+## Table of Contents
+
+- [add-keys-to-git.sh](#add-keys-to-gitsh)
+- [fix-yubikey-perms.sh](#fix-yubikey-permssh)
+- [list-yubikey-ssh-keys.sh](#list-yubikey-ssh-keyssh)
+
+---
+
+## add-keys-to-git.sh
+
+Extracts the SSH public keys from three YubiKey PIV slots and writes them as Git commit signing keys to the corresponding per-context Git config files. Run this after replacing or re-provisioning a YubiKey.
+
+| Slot | Context | Config file |
+|---|---|---|
+| 9a | Personal | `~/.git-naomi` |
+| 9c | Deepgram | `~/.git-dg` |
+| 9e | FreeCodeCamp | `~/.git-fcc` |
+
+### Usage
+
+```bash
+bash bash/yubikey/add-keys-to-git.sh
+```
+
+### Environment Variables
+
+None.
+
+### Data Files
+
+None.
+
+### Notes
+
+- After running, you must upload the new public keys to GitHub (and any other services that verify commit signatures) manually.
+- Requires `ykman` and `ssh-keygen` to be available in your PATH.
+
+---
+
+## fix-yubikey-perms.sh
+
+Repairs YubiKey connectivity in WSL by fixing USB device permissions, restarting smart card services, and applying a polkit policy override that allows smart card access in WSL's "inactive" session context.
+
+### Usage
+
+```bash
+bash bash/yubikey/fix-yubikey-perms.sh
+```
+
+### Environment Variables
+
+None.
+
+### Data Files
+
+None.
+
+### Notes
+
+- Run this script when `ykman` or `yubico-piv-tool` fail with "Failed to connect" or similar errors after attaching the YubiKey via `usbipd`.
+- The polkit fix modifies `/usr/share/polkit-1/actions/org.debian.pcsc-lite.policy` (a backup is created automatically on first run).
+- Requires `sudo` access. Several steps use `sudo` to modify system files and restart services.
+- Requires `lsusb`, `yubico-piv-tool`, `systemctl`, and `gpgconf` to be available.
+
+---
+
+## list-yubikey-ssh-keys.sh
+
+Scans PIV slots 9a, 9c, 9d, and 9e on the connected YubiKey and prints any SSH public keys found, along with the certificate subject label if one is present.
+
+### Usage
+
+```bash
+bash bash/yubikey/list-yubikey-ssh-keys.sh
+```
+
+### Environment Variables
+
+None.
+
+### Data Files
+
+None.
+
+### Notes
+
+- Requires `ykman`, `ssh-keygen`, and `openssl` to be available.
+- Writes a temporary file to `/tmp/yubi_tmp.pem` during execution; it is cleaned up automatically after each slot is processed.