Absolutely! Here's a complete step-by-step guide to set up notmuch with aerc:

## Step 1: Verify notmuch database location

```bash
notmuch config get database.path
```

This will output something like `/home/yourusername/.local/share/mail` or `/home/yourusername/Mail`. **Remember this path** - you'll need it.

## Step 2: Create the notmuch queries file

```bash
mkdir -p ~/.config/aerc
nano ~/.config/aerc/notmuch-queries
```

Paste this content (you can customize later):

```
# Priority folders
Priority 1 - Urgent=tag:priority1 AND tag:inbox
Priority 2 - Work=tag:priority2 AND tag:inbox
Priority 3 - Low=tag:priority3 AND tag:inbox

# Categories
Newsletters=tag:newsletter
Social Media=tag:social
Shopping=tag:shopping
Finance=tag:finance
Travel=tag:travel
Development=tag:dev

# Standard folders
Inbox=tag:inbox AND NOT tag:spam
Unread=tag:unread AND NOT tag:spam
Sent=tag:sent
Spam=tag:spam
Important=tag:important
All Mail=*
```

Save and exit (Ctrl+O, Enter, Ctrl+X).

## Step 3: Update aerc accounts.conf

**First, backup your current config:**
```bash
cp ~/.config/aerc/accounts.conf ~/.config/aerc/accounts.conf.backup
```

**Edit the config:**
```bash
nano ~/.config/aerc/accounts.conf
```

**Replace your IMAP accounts with this** (adjust the database path from Step 1):

```ini
[Proton]
source = notmuch:///home/yourusername/.local/share/mail
query-map = ~/.config/aerc/notmuch-queries
outgoing = smtp://user@127.0.0.1:1025
outgoing-cred-cmd = pass protonmail-bridge
from = Your Name <main@proton.me>
```

**Important notes:**
- Use `notmuch://` (with three slashes) followed by the **absolute path**
- Replace `/home/yourusername/.local/share/mail` with your actual path from Step 1
- Replace `user` with your actual ProtonMail Bridge username
- Replace email addresses with your actual emails

**If you want multiple "from" addresses:**

```ini
[Proton]
source = notmuch:///home/yourusername/.local/share/mail
query-map = ~/.config/aerc/notmuch-queries
outgoing = smtp://user@127.0.0.1:1025
outgoing-cred-cmd = pass protonmail-bridge
from = Your Name <main@proton.me>
aliases = work@proton.me,personal@proton.me
```

Save and exit.

## Step 4: Tag existing emails for processing

```bash
# Tag all mail as 'new' so afew will process it
notmuch tag +new -- '*'

# Verify
notmuch count tag:new
```

Should show your total email count (e.g., 6050).

## Step 5: Run afew to apply filters

```bash
PYTHONWARNINGS="ignore::UserWarning" afew --tag --new --verbose
```

You should see output like:
```
SpamFilter
  Tagging affected 145 message(s)
Filter.1: High priority - Boss and VIPs
  Tagging affected 23 message(s)
Filter.10: Newsletters and subscriptions
  Tagging affected 892 message(s)
...
```

## Step 6: Verify tags were applied

```bash
notmuch count tag:spam
notmuch count tag:newsletter
notmuch count tag:priority1
notmuch count tag:inbox
```

You should see actual numbers now!

## Step 7: Test aerc with notmuch

```bash
aerc
```

**What you should see:**
- Instead of "INBOX", "Sent", etc., you'll see your query-based folders
- "Priority 1 - Urgent"
- "Priority 2 - Work"
- "Newsletters"
- "Inbox"
- etc.

**Navigate folders:**
```
:cf Priority 1 - Urgent<Enter>
```

Or use `j/k` to navigate the folder list and press Enter.

## Step 8: Set up keybindings for quick navigation

```bash
nano ~/.config/aerc/binds.conf
```

Add to the `[messages]` section:

```ini
[messages]
# Quick folder navigation
g1 = :cf Priority 1 - Urgent<Enter>
g2 = :cf Priority 2 - Work<Enter>
g3 = :cf Priority 3 - Low<Enter>
gn = :cf Newsletters<Enter>
gs = :cf Spam<Enter>
gi = :cf Inbox<Enter>
gu = :cf Unread<Enter>
ga = :cf All Mail<Enter>

# Tag management
t = :prompt 'Tag: ' 'tag '
T = :prompt 'Remove tag: ' 'untag '

# Quick tags
!1 = :tag +priority1<Enter>
!2 = :tag +priority2<Enter>
!s = :tag +spam<Enter>
```

## Step 9: Set up automatic mail syncing

```bash
mkdir -p ~/.local/bin
nano ~/.local/bin/sync-mail.sh
```

Paste:

```bash
#!/bin/bash

# Sync from ProtonMail Bridge
mbsync -a

# Index new messages (auto-tags them as 'new')
notmuch new

# Apply filters to new messages
PYTHONWARNINGS="ignore::UserWarning" afew --tag --new

echo "Mail sync complete at $(date)"
```

Make it executable:
```bash
chmod +x ~/.local/bin/sync-mail.sh
```

**Test it:**
```bash
~/.local/bin/sync-mail.sh
```

## Step 10: Automate with systemd (optional)

Create the service:
```bash
mkdir -p ~/.config/systemd/user
nano ~/.config/systemd/user/mailsync.service
```

Paste (replace `yourusername` with your actual username):

```ini
[Unit]
Description=Mailbox sync

[Service]
Type=oneshot
ExecStart=/home/yourusername/.local/bin/sync-mail.sh
```

Create the timer:
```bash
nano ~/.config/systemd/user/mailsync.timer
```

Paste:

```ini
[Unit]
Description=Mailbox sync timer

[Timer]
OnBootSec=2m
OnUnitActiveSec=5m

[Install]
WantedBy=timers.target
```

Enable and start:
```bash
systemctl --user daemon-reload
systemctl --user enable --now mailsync.timer
systemctl --user status mailsync.timer
```

## Step 11: Verify everything works

**Check aerc shows virtual folders:**
```bash
aerc
```

Press `:cf ` and hit Tab - you should see autocomplete for your virtual folders.

**Check folder contents:**
```
:cf Priority 1 - Urgent<Enter>
```

You should see emails that match the filter.

**Check syncing works:**
```bash
# Manually sync
~/.local/bin/sync-mail.sh

# Check timer status
systemctl --user list-timers
```

## Troubleshooting

**Issue: aerc shows "No folders"**
```bash
# Check query-map file exists
cat ~/.config/aerc/notmuch-queries

# Check path in accounts.conf
grep source ~/.config/aerc/accounts.conf
```

**Issue: Folders are empty**
```bash
# Check tags exist
notmuch count tag:inbox
notmuch count tag:newsletter

# If 0, re-run afew
notmuch tag +new -- '*'
afew --tag --new --verbose
```

**Issue: Can't send emails**
```bash
# Test SMTP manually
echo "test" | msmtp -a proton yourmail@proton.me

# Check ProtonMail Bridge is running
pgrep -a bridge
```

**Issue: "Unknown account" error**

Your account name in `accounts.conf` is `[Proton]` but you might be referencing it wrong. Make sure keybindings and commands use the exact name.

## Quick test checklist

- [ ] `notmuch count tag:inbox` shows a number
- [ ] `notmuch count tag:newsletter` shows a number  
- [ ] `cat ~/.config/aerc/notmuch-queries` shows your queries
- [ ] `aerc` shows virtual folders in the sidebar
- [ ] `:cf Inbox<Enter>` in aerc shows emails
- [ ] `~/.local/bin/sync-mail.sh` runs without errors

Once all these work, you're fully set up! Let me know which step gives you trouble.