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>

run.sh

@@ -96,7 +96,7 @@ select_option() {
 
 # Step 1: Select Language
 echo ""
-languages=("TypeScript" "Python")
+languages=("TypeScript" "Python" "Bash")
 select_option "Select a language:" "${languages[@]}"
 lang_index=$?
 language="${languages[$lang_index]}"
@@ -109,15 +109,16 @@ if [ "$language" == "TypeScript" ]; then
     runner="pnpm tsx"
     # Get subdirectories as categories (excluding utils and interfaces)
     mapfile -t categories < <(find "$script_dir" -mindepth 1 -maxdepth 1 -type d ! -name 'utils' ! -name 'interfaces' -exec basename {} \; | sort)
-else
+elif [ "$language" == "Python" ]; then
     script_dir="python"
     runner="uv run python"
     # Get subdirectories as categories (excluding __pycache__ and .venv)
     mapfile -t categories < <(find "$script_dir" -mindepth 1 -maxdepth 1 -type d ! -name '__pycache__' ! -name '.venv' ! -name '*.egg-info' -exec basename {} \; | sort)
-    # Add "Root Scripts" option for Python files in root
-    if ls "$script_dir"/*.py &>/dev/null 2>&1; then
-        categories=("Root Scripts" "${categories[@]}")
-    fi
+else
+    script_dir="bash"
+    runner="bash"
+    # Get subdirectories as categories
+    mapfile -t categories < <(find "$script_dir" -mindepth 1 -maxdepth 1 -type d -exec basename {} \; | sort)
 fi
 
 if [ ${#categories[@]} -eq 0 ]; then
@@ -132,12 +133,12 @@ category="${categories[$cat_index]}"
 echo -e "\n  ${GREEN}$STAR Selected: ${WHITE}$category${RESET}\n"
 
 # Step 3: Get scripts in category
-if [ "$category" == "Root Scripts" ]; then
-    search_dir="$script_dir"
-    mapfile -t scripts < <(find "$search_dir" -maxdepth 1 -name "*.py" -exec basename {} \; | sort)
-elif [ "$language" == "TypeScript" ]; then
+if [ "$language" == "TypeScript" ]; then
     search_dir="$script_dir/$category"
     mapfile -t scripts < <(find "$search_dir" -name "*.ts" -exec basename {} \; | sort)
+elif [ "$language" == "Bash" ]; then
+    search_dir="$script_dir/$category"
+    mapfile -t scripts < <(find "$search_dir" -name "*.sh" -exec basename {} \; | sort)
 else
     search_dir="$script_dir/$category"
     mapfile -t scripts < <(find "$search_dir" -name "*.py" ! -name "__init__.py" -exec basename {} \; | sort)
@@ -155,8 +156,8 @@ script="${scripts[$script_index]}"
 echo -e "\n  ${GREEN}$STAR Selected: ${WHITE}$script${RESET}\n"
 
 # Build the full script path
-if [ "$category" == "Root Scripts" ]; then
-    script_path="$script"
+if [ "$language" == "Bash" ]; then
+    script_path="bash/$category/$script"
 elif [ "$language" == "TypeScript" ]; then
     script_path="src/$category/$script"
 else
@@ -178,6 +179,9 @@ if [ "$language" == "TypeScript" ]; then
     cd typescript
     echo -e "  ${DIM}$ op run --env-file=../prod.env -- $runner $script_path${RESET}\n"
     op run --env-file=../prod.env --no-masking -- $runner "$script_path"
+elif [ "$language" == "Bash" ]; then
+    echo -e "  ${DIM}$ $runner $script_path${RESET}\n"
+    $runner "$script_path"
 else
     cd python
     echo -e "  ${DIM}$ op run --env-file=../prod.env -- $runner $script_path${RESET}\n"