Exclude node_modules (and more) from timemachine, use launchd to scan the Project directory on a regular basis, for example meanwhile you are having siesta. Put this file in ~/Library/LaunchAgents and call `launchctl load ~/Library/LaunchAgents/com.user.time-machine-exclude-node-modules-job.plist`

com.user.time-machine-exclude-node-modules-job.plist

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
  <key>Label</key>
  <string>com.user.time-machine-exclude-node-modules-job</string>
  <key>RunAtLoad</key>
  <false/>
  <key>KeepAlive</key>
  <false/>
  <key>ProgramArguments</key>
  <array>
    <string>/bin/bash</string>
    <string>-c</string>
    <string>cd "$HOME/Projects" &amp;&amp; find $(pwd) -type d \( -name vendor -o -name node_modules \) -prune -exec tmutil addexclusion {} \; -exec tmutil isexcluded {} \;</string>
  </array>
  <key>StartCalendarInterval</key>
  <dict>
    <key>Hour</key>
    <integer>13</integer>
    <key>Minute</key>
    <integer>15</integer>
  </dict>
  <!-- Debug logging  -->
  <!--
  <key>StandardOutPath</key>
  <string>/tmp/launchd.log</string>
  <key>StandardErrorPath</key>
  <string>/tmp/launchd.log</string>
  -->
</dict>
</plist>