File layout

In the vault

Path	What it is
**/*.md	Your notes
**/CLAUDE.md, AGENTS.md, GEMINI.md	Per-folder context, named for the active assistant
.<assistant>/skills/mindex-note-types/SKILL.md	Your types, written for the CLI
.mindex/cache.json	The index — derived, rebuilt if deleted
.mindex/settings.json	Settings belonging to this vault
.mindex/policy.json	Vault policy
.mindex/types/<id>.md	Note types you created or edited
.mindex/templates/context-template.md	Your version of the context template
.mindex/history/	A version log per note, with the contents compressed beside it
.mindex/comments/	Comment threads, one file per commented note
.mindex/rewrites/	Rewrites offered in the editor and not yet answered
.mindex/chat/	The conversations in the right sidebar
.mindex/tmp/	Staging for atomic writes — derived

Attachments are ordinary files wherever you put them. Nothing is copied into a hidden store.

What is committed

When Mindex sets a vault up for Git it ignores the whole metadata folder:

.mindex/
.DS_Store
node_modules/

So the notes and the context files are published and nothing else — history, comments, chat and settings stay on the machine they were made on.

Two of those folders are worth sharing if the vault is a shared one: the types you created and your version of the context template are part of how the vault works rather than a record of how you used it. Un-ignore them yourself:

.mindex/
!.mindex/types/
!.mindex/templates/

What happens if you delete .mindex/

The vault still opens, and every note is untouched. The index is rebuilt from the files; the settings go back to defaults; local history, comments and any type you had created are gone.

The context filename follows the assistant

Switching assistants renames the existing context files so the new CLI finds them. See Folder context.