HarnessKit and your files
HarnessKit is an editor for your agents’ own directories, not a host for them. Each agent keeps reading its own files, in its own format, whether HarnessKit is running or not. HarnessKit reads those files to show you what is installed. It writes to them when you install, enable, disable or delete something.
HarnessKit keeps one file of its own that matters: ~/.harnesskit/metadata.db. It holds facts that have no place in an agent’s files, such as where a skill came from and its audit results. It also holds snapshots, exact copies of MCP servers and hooks you disabled on agents that have no off switch of their own. No agent reads this file.
One test shows the model at work. Remove HarnessKit, and every agent keeps the setup it had. The exceptions are the items you had turned off, which Managing files in place lists.
Read in this order
Section titled “Read in this order”Read the first four pages in order, since each builds on the one before it. The last three stand on their own.