Data directory

Override with CRYSTAL_HOME or --home.

~/.crystal/
  binaries/code/CrystalCode (CrystalCode.exe on Windows)
  config.json
  providers.json
  credentials.json
  permissions.json
  trusted.json
  access.json
  instructions.md
  AGENTS.md
  prompts/
    work.md
    plan.md
    review.md
    review.user.md
    topic.md
    compaction.system.md
    compaction.user.md
    image.system.md
    image.user.md
  promptsets/
    concise/
      prompt.json
      work.md
      plan.md
      review.md
      review.user.md
      topic.md
      compaction.system.md
      compaction.user.md
      image.system.md
      image.user.md
  prompt-attachments/
    <name>/
      prompt.json
      work.md
      plan.md
      review.md
  skill/<name>/SKILL.md
  skills/<name>/SKILL.md
  tools/<directory>/tools.json
  data/tools/<directory>/
  plugins/<directory>/plugin.json
  data/plugins/<directory>/
  sessions/<id>.json
  logs/

Project overlay (named prompts, prompt attachments, Crystal skills, tool sets, and plugins of the same directory name win over home):

<workspace>/.crystal/
  instructions.md
  prompts/
    work.md
    plan.md
    review.md
    review.user.md
    topic.md
    compaction.system.md
    compaction.user.md
    image.system.md
    image.user.md
  prompt-attachments/
    <name>/
      prompt.json
      work.md
      plan.md
      review.md
  skill/<name>/SKILL.md
  skills/<name>/SKILL.md
  tools/<directory>/tools.json
  plugins/<directory>/plugin.json
  data/tools/<directory>/
  data/plugins/<directory>/
<workspace>/.crystal.md
<workspace>/AGENTS.md

config.json is not part of the project overlay. Workspace-level configuration is deferred.

access.json stores default extra directories for each canonical workspace root.

Event	What happens to the defaults
New session, /clear, /fork, successful /cd or /space	Copies the defaults into the session
/resume	Keeps the saved rules. Does not add defaults back
Any --allow-read or --allow-write	Replaces the defaults for this process. Not saved

A missing directory or a credential path is skipped with an error and left in the file. A corrupt file, or two modes for one directory, seeds nothing. The session still opens.

Plugins and tool sets keep runtime data under data/, split by kind.

Root	Path
Global	~/.crystal/data/{plugins|tools}/<directory>, shared across workspaces
Project	<workspace>/.crystal/data/{plugins|tools}/<directory>

The host creates both the first time the extension receives them, at plugin attach or before a tool call. They are separate from the install trees and are not a secret store.

plugins/<directory>/plugin.json loads one operator plugin. Dotnet tool sets still load class libraries from the tool-set directory only. See Plugins.