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/remove_member.py

@@ -0,0 +1,247 @@
+#!/usr/bin/env python3
+"""Remove a member from the Spring 2026 Cohort.
+
+This script:
+1. Removes from team_assignments.json (so activity checker stops tracking them)
+2. Removes from discord_to_github.json
+3. Removes from GitHub teams
+4. Removes Discord roles
+5. Sends a message to the team channel announcing the removal
+6. Outputs notes to add to COHORT_NOTES.md
+
+Usage:
+    python remove_member.py <discord_id>
+"""
+
+import asyncio
+import json
+import os
+import sys
+from datetime import datetime, timezone
+from pathlib import Path
+
+import aiohttp
+
+DATA_DIR = Path(__file__).parent.parent.parent / "data"
+
+DISCORD_BOT_TOKEN = os.environ["DISCORD_BOT_TOKEN"]
+DISCORD_API_BASE = "https://discord.com/api/v10"
+DISCORD_GUILD_ID = "692816967895220344"
+COHORT_ROLE_ID = "1464316447591985194"
+
+TEXT_CHANNEL_IDS = {
+    "Jade Jasmine": "1464316501573107886",
+    "Crimson Dahlia": "1464316744909852682",
+    "Rose Camellia": "1464316751268286611",
+    "Amber Wisteria": "1464316761410113641",
+    "Ivory Orchid": "1464316770889240730",
+    "Teal Iris": "1464316776459407448",
+    "Peach Gardenia": "1464316785040953543",
+    "Violet Carnation": "1464316805261824032",
+    "Azure Lotus": "1464316814455472139",
+    "Coral Sunflower": "1464316819711066263",
+    "Indigo Tulip": "1464316826384072925",
+    "Scarlet Hydrangea": "1464316839306985506",
+    "Mint Narcissus": "1464316844251807952",
+    "Sage Marigold": "1464316850669093040",
+}
+
+
+class MemberRemover:
+    """Handles the complete removal of a cohort member."""
+
+    def __init__(self, discord_id: str) -> None:
+        self.discord_id = discord_id
+        self.headers = {
+            "Authorization": f"Bot {DISCORD_BOT_TOKEN}",
+            "Content-Type": "application/json",
+        }
+        self.session: aiohttp.ClientSession | None = None
+        self.github_username: str | None = None
+        self.team_name: str | None = None
+        self.role: str | None = None
+        self.team_role_id: str | None = None
+
+    async def __aenter__(self) -> "MemberRemover":
+        self.session = aiohttp.ClientSession()
+        return self
+
+    async def __aexit__(
+        self, exc_type: object, exc_val: object, exc_tb: object
+    ) -> None:
+        if self.session:
+            await self.session.close()
+
+    def find_member_info(self) -> bool:
+        """Find which team the member is on and their role."""
+        with open(DATA_DIR / "team_assignments.json") as f:
+            teams = json.load(f)
+
+        for team in teams:
+            if self.discord_id in team["leaders"]:
+                self.team_name = team["name"]
+                self.role = "leader"
+                return True
+            if self.discord_id in team["participants"]:
+                self.team_name = team["name"]
+                self.role = "participant"
+                return True
+
+        return False
+
+    def remove_from_team_assignments(self) -> None:
+        """Remove member from team_assignments.json."""
+        with open(DATA_DIR / "team_assignments.json") as f:
+            teams = json.load(f)
+
+        for team in teams:
+            if self.discord_id in team["leaders"]:
+                team["leaders"].remove(self.discord_id)
+                print(
+                    f"✅ Removed from {team['name']} leaders in team_assignments.json"
+                )
+            elif self.discord_id in team["participants"]:
+                team["participants"].remove(self.discord_id)
+                print(
+                    f"✅ Removed from {team['name']} participants in team_assignments.json"
+                )
+
+        with open(DATA_DIR / "team_assignments.json", "w") as f:
+            json.dump(teams, f, indent=2)
+
+    def remove_from_discord_to_github(self) -> None:
+        """Remove member from discord_to_github.json."""
+        with open(DATA_DIR / "discord_to_github.json") as f:
+            mappings = json.load(f)
+
+        if self.discord_id in mappings:
+            self.github_username = mappings[self.discord_id]
+            del mappings[self.discord_id]
+
+            with open(DATA_DIR / "discord_to_github.json", "w") as f:
+                json.dump(mappings, f, indent=2)
+
+            print(f"✅ Removed {self.github_username} from discord_to_github.json")
+        else:
+            print("⚠️  No GitHub username found in discord_to_github.json")
+
+    async def remove_from_github_teams(self) -> None:
+        """Print instructions to remove member from GitHub organization teams."""
+        if not self.github_username:
+            print("⚠️  Skipping GitHub removal (no username)")
+            return
+
+        print(f"ℹ️  Please manually remove {self.github_username} from GitHub teams:")
+        print(f"   - Team: {self.team_name}")
+        if self.role == "leader":
+            print(f"   - Team: {self.team_name} Leaders")
+
+    async def remove_discord_roles(self) -> None:
+        """Remove Discord roles from the member."""
+        with open(DATA_DIR / "team_message_ids.json") as f:
+            team_message_data = json.load(f)
+
+        if self.team_name not in team_message_data:
+            print(f"⚠️  Could not find role ID for team {self.team_name}")
+            return
+
+        self.team_role_id = team_message_data[self.team_name]["role_id"]
+
+        url = (
+            f"{DISCORD_API_BASE}/guilds/{DISCORD_GUILD_ID}"
+            f"/members/{self.discord_id}/roles/{self.team_role_id}"
+        )
+        async with self.session.delete(url, headers=self.headers) as response:
+            if response.status == 204:
+                print(f"✅ Removed {self.team_name} Discord role")
+            else:
+                print(f"❌ Failed to remove team role: {response.status}")
+
+        url = (
+            f"{DISCORD_API_BASE}/guilds/{DISCORD_GUILD_ID}"
+            f"/members/{self.discord_id}/roles/{COHORT_ROLE_ID}"
+        )
+        async with self.session.delete(url, headers=self.headers) as response:
+            if response.status == 204:
+                print("✅ Removed Spring 2026 Cohort Discord role")
+            else:
+                print(f"❌ Failed to remove cohort role: {response.status}")
+
+    async def send_team_message(self) -> None:
+        """Send a message to the team channel announcing the removal."""
+        channel_id = TEXT_CHANNEL_IDS[self.team_name]
+
+        message = (
+            f"<@{self.discord_id}> has been removed from the cohort for inactivity."
+        )
+
+        url = f"{DISCORD_API_BASE}/channels/{channel_id}/messages"
+        data = {"content": message}
+
+        async with self.session.post(url, headers=self.headers, json=data) as response:
+            if response.status == 200:
+                print(f"✅ Sent removal message to {self.team_name} channel")
+            else:
+                print(f"❌ Failed to send message: {response.status}")
+
+    def generate_cohort_notes(self) -> str:
+        """Generate text to add to COHORT_NOTES.md."""
+        today = datetime.now(timezone.utc).strftime("%Y-%m-%d")
+
+        notes = f"\n## {today} - Member Removal\n\n"
+        notes += "| Discord ID | GitHub Username | Team | Role |\n"
+        notes += "|------------|-----------------|------|------|\n"
+        notes += (
+            f"| {self.discord_id} | {self.github_username or '-'} "
+            f"| {self.team_name} | {self.role.capitalize()} |\n"
+        )
+
+        return notes
+
+
+async def main() -> None:
+    """Remove a member from the cohort."""
+    if len(sys.argv) != 2:
+        print("Usage: python remove_member.py <discord_id>")
+        sys.exit(1)
+
+    discord_id = sys.argv[1]
+
+    async with MemberRemover(discord_id) as remover:
+        if not remover.find_member_info():
+            print(f"❌ Discord ID {discord_id} not found in any team")
+            sys.exit(1)
+
+        print("\n📋 Found member:")
+        print(f"   Discord ID: {discord_id}")
+        print(f"   Team: {remover.team_name}")
+        print(f"   Role: {remover.role}")
+        print()
+
+        confirm = input("Proceed with removal? (yes/no): ")
+        if confirm.lower() != "yes":
+            print("❌ Removal cancelled")
+            sys.exit(0)
+
+        print("\n🚀 Starting removal process...\n")
+
+        remover.remove_from_team_assignments()
+        remover.remove_from_discord_to_github()
+
+        await remover.remove_from_github_teams()
+
+        await remover.remove_discord_roles()
+
+        await remover.send_team_message()
+
+        print("\n" + "=" * 80)
+        print("📝 Add this to COHORT_NOTES.md:")
+        print("=" * 80)
+        print(remover.generate_cohort_notes())
+        print("=" * 80)
+
+        print("\n✅ Member removal complete!")
+
+
+if __name__ == "__main__":
+    asyncio.run(main())