8. How it works inside
8.2 The kit's folders on disk
projects and data: what is in each folder, which files are yours, which belong to the kit and which are protected.
In short
- Everything is in the kit folder: the executable, projects (yours) and data (the kit's).
- In data the programs are separated by system; the rest is shared between Windows, macOS and Linux.
- The folders with passwords can be read only by your user (on NTFS drives).
The folders
- Projects folder
projects\- Shared agents
data\agents\- Database data
data\db\- Database backups
data\projects\<project>\private\backups\
| Folder or file | What it contains |
|---|---|
<kit folder>\ | The folder that contains the executable, for example D:\Atollo. |
Atollo.exe | The only program: it is the app with the window and also the command line. On macOS Atollo.app, on Linux the AppImage. |
projects\ | Your projects, one folder each. It is yours: the kit does not write there unless you ask. |
data\ | Everything that belongs to the kit. |
app\ | The app's state: settings.json (Settings), secrets\ (the Gemini key, the local models server's key and the Hugging Face token, protected), llm.json and llm\presets.ini (the local models server), ca-bundle.pem (the certificates, when Settings has a PEM file), components.txt (chosen components), versions\ (installed versions), logs\, services.json and servers.json (databases and web servers, with the ports of every version and every pool), terminals.json, frameworks.json, root.txt (last kit folder), safe-directory.txt (the last safe.directory the kit wrote). |
app\db\ | Database administrator passwords and mysql logins. Protected: only your user can read it. |
app\diagnostics\ | The zips of “Export diagnostics” (atollo-diagnostica-<date-time>.zip), to attach to a report: secrets masked, they stay on the PC. |
apps\<system>\ | The programs, by system (win32-x64, darwin-arm64…), one folder per component and per version. |
projects\<project>\ | The kit's data for each project: dev-settings.json (versions, extensions, favorites), ports.json (the ports of its actions), Apache and Caddy configurations (your directives in apache\conf.d\*.conf and caddy\conf.d\*.caddy apply both to its own server and in a pool), private\ (database passwords and backups, protected). |
db\<mysql|mongodb>\<version>\ | The databases' data, one folder per version. |
models\gguf\<owner>--<name>\ | The local models (GGUF files), one folder per Hugging Face repository, a single copy for Windows, macOS and Linux; atollo.json says what the kit downloaded. |
servers\<pool>\ | The generated configurations of the shared web servers. |
agents\ | What the agents share: AGENTS.md, skills\, mcp.json, and the sync state in .sync\. |
antigravity\ | The Antigravity sign-in kept in the kit (keyring.json). |
home\ | The “user folder” of the kit's programs: .claude, .codex, .gemini, .pi (agent profiles), .gitconfig, .npmrc, AppData (on Windows). |
gh\ | The GitHub CLI sign-in (hosts.yml). |
vscodium-server\ | Settings and extensions of the editor server. |
kit\ | Files the kit rewrites at every start: the PowerShell profile, helper commands (agy, mysql, gradle). |
cache\ | Cache of the package managers (npm, pip, uv, Composer, Go, NuGet…) and of GitHub's responses. It can be deleted. |
python-user\, npm-global\, composer\, go\, gradle\… | Packages and tools installed globally with pip, npm, Composer, Go and the others. |
tmp\ | Temporary files, when Settings wants them in the kit. |
webview2\ | The data of the app window. |
What is yours and what is the kit's
| You can edit by hand | Better left to the kit |
|---|---|
| Everything in projects; data\agents (instructions, skills, mcp.json); data\home\.gitconfig | data\app, data\apps, data\kit, data\servers, data\db: the kit manages them, and some are rewritten at every start |
Under the hood
- Protected folders (only your user, on NTFS; permissions 700 on macOS and Linux): data\app\db, data\app\secrets, data\projects\<project>\private, data\agents\claude, data\tmp when it is Claude's temporary folder.
- On exFAT and FAT32 permissions do not exist: the kit works, but those folders are not protected.
- Configuration files are written safely: first a temporary file, then the replacement, so an interruption does not leave half-written files.
- data\kit is rewritten at every start: do not put your own files there.