Optimization & Tips: Maximize Your Stack

# Process all new papers at 2am
0 2 * * * ~/scripts/batch-summarize-zotero.sh

# In Zotero Settings
Settings → Sync → ✗ Sync attachment files

# Configure WebDAV in Zotero
Settings → Sync → File Syncing → WebDAV
URL: https://your-university.sharepoint.com/webdav

---
date: {{date:YYYY-MM-DD}}
---

# Research Log: {{date:MMMM DD, YYYY}}

## Papers Read Today
```dataview
LIST
FROM "Literature Notes"
WHERE created = date({{date:YYYY-MM-DD}})

**Usage**: Press `Ctrl+T` (or `Cmd+T`) daily to create tracking log from template.

### Weekly Literature Digest

Create `~/scripts/weekly-digest.sh`:

```bash
#!/bin/bash
CURRENT_WEEK=$(date +%Y-W%U)

gemini << EOF > ~/Obsidian/Digests/$CURRENT_WEEK-digest.md
Create a weekly research digest from these papers:

$(find ~/Obsidian/Literature\ Notes -mtime -7 -name "*.md" -exec cat {} \;)

Format:
# Week of $(date +%B\ %d,\ %Y)

## Key Themes This Week
## Important Findings
## Papers to Prioritize (top 3)
## Connections to My Research
EOF

chmod +x ~/scripts/weekly-digest.sh

# Run every Monday at 9am
0 9 * * 1 ~/scripts/weekly-digest.sh

# ~/scripts/export-citations.sh
#!/bin/bash

# Export from Zotero via Better BibTeX
# Assumes Better BibTeX auto-export is configured

# Verify export is recent (less than 24 hours old)
if [ $(find ~/Documents/library.bib -mtime -1) ]; then
    echo "Citations up to date"
else
    echo "WARNING: library.bib is stale. Re-export from Zotero."
fi

#!/bin/bash
# .git/hooks/pre-commit

~/scripts/export-citations.sh

# Check when library.bib was last updated
ls -l ~/Documents/library.bib

# If stale, re-export from Zotero
# In Zotero: Right-click library → Export Collection
# Format: Better BibTeX
# ✓ Keep updated

Zotero → Preferences → Better BibTeX → Automatic Export
→ Add path: ~/Documents/library.bib
→ On Change

.obsidian/workspace
.obsidian/workspace.json
.obsidian/cache
.trash/

# Before editing
git pull

# After editing
git add .
git commit -m "Add notes on [topic]"
git push

chmod +x ~/scripts/*.sh

ls -l ~/scripts/
# Should show: -rwxr-xr-x (executable flag set)

# ~/scripts/check-quota.sh
#!/bin/bash

QUOTA_FILE=~/.gemini-quota
TODAY=$(date +%Y-%m-%d)

# Initialize quota file if doesn't exist
if [ ! -f $QUOTA_FILE ] || [ "$(head -n1 $QUOTA_FILE)" != "$TODAY" ]; then
    echo "$TODAY" > $QUOTA_FILE
    echo "0" >> $QUOTA_FILE
fi

# Read current count
COUNT=$(sed -n '2p' $QUOTA_FILE)

if [ $COUNT -ge 25 ]; then
    echo "ERROR: Daily quota exceeded ($COUNT/25)"
    exit 1
else
    echo "Quota remaining: $((25 - COUNT))/25"
fi

# Check quota before processing
if ! ~/scripts/check-quota.sh; then
    echo "Skipping batch processing - quota exhausted"
    exit 0
fi

# Increment counter after successful request
COUNT=$(sed -n '2p' ~/.gemini-quota)
echo "$(head -n1 ~/.gemini-quota)" > ~/.gemini-quota
echo "$((COUNT + 1))" >> ~/.gemini-quota

Settings → Files & Links:
✗ Automatically update internal links
✗ Detect all file extensions

Settings → Core Plugins:
✗ Backlinks (if not used)
✗ Outgoing links (if not used)

{
  "alwaysUpdateLinks": false,
  "strictLineBreaks": true,
  "foldHeading": true,
  "foldIndent": true
}

# In Zotero
Tools → Preferences → Advanced → Files and Folders
→ Database Maintenance → Optimize Database

Settings → Search:
✗ Index PDFs