docs(installation): limit REA to one project or agent profile

Document existing Claude Code profile and per-project installation workflows, including scoped maintenance, backups, caller metadata and Windows commands. Clarify authentication storage and the filesystem/network restrictions required for enforced separation.

Validated 68 boundary tests, docs checks, formatting, typecheck/lint and two real REA setup dry-runs with zero applied actions or profile writes. Native Claude sessions, PowerShell execution and enforcement policies were not tested. Setup automation remains separate in #2187.

Co-authored-by: William Blair <60581672+williamblair333@users.noreply.github.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>
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@ -129,6 +129,150 @@ Setup pins package-runner MCP registrations to the exact installed REA version,
installs the matching skill and on-demand references in the same plan, and adds
`startup_timeout_sec = 30` for Codex and Grok Build.
## Limit REA to one project or agent profile
Setup registers REA for the whole client. For Claude Code it writes
`mcpServers.rea` in `~/.claude.json` and installs the bundled skill under
`~/.claude/skills`, so every project that Claude Code opens can call REA. To
offer REA's tools only where they're wanted, use one of the routes below.
Both routes control which sessions discover REA's MCP server and skill. They
leave shell commands, filesystem access and network access available. An agent
under the same OS account can run `rea` from `PATH` or `npx` and read other
profiles and REA output. For clean-room separation, use an implementation
environment with filesystem and network restrictions that prevent reading or
fetching REA, the target and analysis output, including through shared
installations and package registries. A separate account or container must
enforce those restrictions.
For Claude Code, check existing default-profile state before choosing either
route. Setup is additive: a previous user-level REA registration and personal
skill remain active in other projects. Back up the default configuration and
REA skill first, then, with `CLAUDE_CONFIG_DIR` unset, remove the REA user
registration with `claude mcp remove --scope user rea` and remove the known
REA-installed `~/.claude/skills/reverse-engineer-anything` directory. Preserve
unrelated registrations and skills. `rea uninstall` applies to other clients
as well, so it is broader than this Claude-only migration.
**A separate Claude Code profile.** Claude Code keeps settings, skills and session
history under `CLAUDE_CONFIG_DIR`. Setup follows the same
variable: it writes the registration to `$CLAUDE_CONFIG_DIR/.claude.json` and
the skill to `$CLAUDE_CONFIG_DIR/skills`.
```bash
CLAUDE_CONFIG_DIR=~/.claude-rea npx rea-agents setup --client claude_code
CLAUDE_CONFIG_DIR=~/.claude-rea claude
```
A new profile may need authentication. Console sign-ins without an API key are
stored outside `CLAUDE_CONFIG_DIR`; see
[Claude Code authentication](https://code.claude.com/docs/en/authentication#log-in-with-multiple-accounts).
Sessions started without the variable use the default profile's registration,
skill and history.
Inline assignments apply only to that command. Keep the same prefix for every
profile check, setup rerun, update, or removal; bare commands use the current
environment and can otherwise inspect or recreate default-profile state:
```bash
CLAUDE_CONFIG_DIR=~/.claude-rea claude mcp list
CLAUDE_CONFIG_DIR=~/.claude-rea npx rea-agents doctor --client claude_code --skill --json
CLAUDE_CONFIG_DIR=~/.claude-rea npx -y rea-agents@latest setup --client claude_code --dry-run
```
After reviewing an update plan, rerun that same prefixed setup command without
`--dry-run` and approve its exact changes. Profile removal likewise needs the
prefix on `claude mcp remove --scope user rea` and any `rea uninstall` command;
keep the broader client scope of uninstall in mind. Restart the selected
profile after changing its pinned registration.
`claude mcp remove` removes only the registration. To remove REA from this
profile without running the broader uninstall flow, first back up the profile's
REA-managed skill directory, then remove
`$CLAUDE_CONFIG_DIR/skills/reverse-engineer-anything` as well. Keep other skills
in the profile intact.
The commands above use POSIX shell assignment syntax. In native Windows
PowerShell, select the profile for the whole setup/launch/check session and
restore the previous selection afterward:
```powershell
$previousClaudeConfigDir = $env:CLAUDE_CONFIG_DIR
try {
$env:CLAUDE_CONFIG_DIR = Join-Path $HOME ".claude-rea"
npx rea-agents setup --client claude_code
claude mcp list
npx rea-agents doctor --client claude_code --skill --json
npx -y rea-agents@latest setup --client claude_code --dry-run
# After reviewing the plan, repeat setup without --dry-run and approve it.
claude
# Profile removal, when intended, also belongs inside this selected scope:
# claude mcp remove --scope user rea
} finally {
if ($null -eq $previousClaudeConfigDir) {
Remove-Item Env:CLAUDE_CONFIG_DIR -ErrorAction SilentlyContinue
} else {
$env:CLAUDE_CONFIG_DIR = $previousClaudeConfigDir
}
}
```
Use PowerShell for these Windows examples rather than pasting POSIX assignments
into cmd.exe. Keep profile updates, readiness checks and removal inside the
same selected environment; the `finally` block restores the previous profile
or unsets the variable when it was absent.
**One project.** Install without configuring Claude Code: use the curl
installer's `--no-setup`, or run setup only for other clients. Then register
REA from the project directory at Claude Code's local scope.
This route uses the default Claude profile. Keep `CLAUDE_CONFIG_DIR` unset for
the entire local lifecycle: registration, backup, listing, version replacement
and removal. In POSIX shells run `unset CLAUDE_CONFIG_DIR`; in PowerShell run
`Remove-Item Env:CLAUDE_CONFIG_DIR -ErrorAction SilentlyContinue` before these
commands. Record an existing selection first if you intend to restore it after
finishing. The configuration path below is the default profile's
`~/.claude.json`; a different active profile uses its own config root instead.
Register with the variable unset:
<!-- x-release-please-start-version -->
```bash
claude mcp add --scope local rea -- npx -y rea-agents@6.4.0 mcp
```
On native Windows, use the same project directory and wrap the package-runner
shim so the stdio client can launch it:
```powershell
claude mcp add --scope local rea -- cmd.exe /d /c npx -y rea-agents@6.4.0 mcp
```
<!-- x-release-please-end -->
Local scope stores the entry under that directory's path in `~/.claude.json`,
so other projects don't load it. This route doesn't install the bundled skill.
Avoid `--scope project`, which writes `.mcp.json` into the repository where it
can be committed or copied. `rea doctor` and `rea uninstall` read only the
user-level entry, so they don't report or remove a local-scope registration;
remove it with `claude mcp remove --scope local rea` from the same directory.
`rea update` doesn't refresh it either, so it stays on the version it names.
To move it to a newer release, first back up the project entry in
`~/.claude.json` and record its environment and other metadata. In particular,
preserve caller-selected overrides such as `REA_MCP_INPUT_SCHEMA_PROFILE` and
`REA_MCP_MAX_RESPONSE_BYTES`. Run `claude mcp remove --scope local rea` from the
same directory, then recreate it with the platform-appropriate command above
and the new version. Reapply every recorded environment value with Claude
Code's `mcp add --env NAME=value` options and restore any other retained entry
metadata before restarting the project session. Removal and re-addition do not
preserve these values automatically. Running setup for Claude Code instead
would add a user-level entry for every project.
Check the separate profile with the prefixed `claude mcp list` above and compare
with the default profile with `CLAUDE_CONFIG_DIR` unset. For local scope, run
`claude mcp list` from the selected project and again from another project.
## Check readiness for your task
Run `rea doctor` when you need diagnosis. It reads host prerequisites and agent