fix(security): standardize paperclipai CLI guidance on safe npx path (#11343)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Paperclip provides CLI guidance to agents and operators through
documentation and runtime messages.
> - Content-bearing `pnpm paperclipai` examples send arguments through a
shell.
> - Shell evaluation can execute command substitutions in untrusted
argument content.
> - Runtime hostname guidance can also place request-derived content
inside a shell command.
> - This pull request uses `npx paperclipai` for content-bearing
guidance and uses a static hostname placeholder.
> - The benefit is safer copy-paste guidance for agents and operators.

## Linked Issues or Issue Description

**Issue type**
Incorrect information

**Where is the issue?**
CLI guidance in `doc/CLI.md`, `skills/paperclip/SKILL.md`,
documentation, and runtime-generated hints.

**What's wrong?**
Content-bearing `pnpm paperclipai` commands can pass argument text
through `/bin/sh`. Shell command substitution in an argument can execute
before the CLI receives the value.

**Suggested fix**
Use `npx paperclipai` for content-bearing commands. Use a static
`<host>` placeholder when runtime guidance displays the allowed-hostname
command.

## What Changed

- Replace content-bearing `pnpm paperclipai` examples with `npx
paperclipai` across the documentation and agent-facing guidance.
- Update runtime-generated CLI hints to use a static `<host>`
placeholder.
- Add safety notes to `doc/CLI.md` and `skills/paperclip/SKILL.md`.
- Add scans and regression tests for unsafe invocation and hostile
hostname headers.
- Keep fixed lifecycle commands and `pnpm --filter @paperclipai/*` build
commands unchanged.

## Verification

- Run `tsc --noEmit` for the changed server files.
- Run `cli-invocation-safety.test.ts`.
- Run `private-hostname-guard.test.ts`.
- Confirm that hostile hostname headers do not enter shown shell
commands.
- Confirm that the three commits contain the required Paperclip
co-author trailer.

## Risks

- This change updates documentation and diagnostic text across many
surfaces.
- Fixed lifecycle and setup commands remain unchanged.
- The tests fail if content-bearing `pnpm paperclipai` guidance returns.
- The change does not alter the CLI argument parser.

## Model Used

OpenAI Codex, GPT-5, tool use, code execution, and repository review
assistance.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

docs/deploy/deployment-modes.md

@@ -42,7 +42,7 @@ pnpm paperclipai onboard
 Allow custom Tailscale hostnames:
 
 ```sh
-pnpm paperclipai allowed-hostname my-machine
+pnpm exec paperclipai allowed-hostname my-machine
 ```
 
 ### `authenticated` + `public`

docs/deploy/local-development.md

@@ -64,7 +64,7 @@ pnpm dev --authenticated-private
 Allow additional private hostnames:
 
 ```sh
-pnpm paperclipai allowed-hostname dotta-macbook-pro
+pnpm exec paperclipai allowed-hostname dotta-macbook-pro
 ```
 
 For full setup and troubleshooting, see [Tailscale Private Access](/deploy/tailscale-private-access).

docs/deploy/secrets.md

@@ -203,7 +203,7 @@ Validate secrets config:
 
 ```sh
 pnpm paperclipai doctor
-pnpm paperclipai secrets doctor --company-id <company-id>
+pnpm exec paperclipai secrets doctor --company-id <company-id>
 ```
 
 ### Environment Overrides
@@ -475,8 +475,8 @@ store.
 If you have existing agents with inline API keys in their config, migrate them to encrypted secret refs:
 
 ```sh
-pnpm paperclipai secrets migrate-inline-env --company-id <company-id>
-pnpm paperclipai secrets migrate-inline-env --company-id <company-id> --apply
+pnpm exec paperclipai secrets migrate-inline-env --company-id <company-id>
+pnpm exec paperclipai secrets migrate-inline-env --company-id <company-id> --apply
 
 # low-level script for direct database maintenance
 pnpm secrets:migrate-inline-env         # dry run
@@ -493,7 +493,7 @@ Company exports include only environment declarations. They do not include
 secret IDs, provider references, encrypted material, or plaintext values.
 
 ```sh
-pnpm paperclipai secrets declarations --company-id <company-id> --kind secret
+pnpm exec paperclipai secrets declarations --company-id <company-id> --kind secret
 ```
 
 Before importing a package into another instance, use those declarations to

docs/deploy/tailscale-private-access.md

@@ -58,7 +58,7 @@ http://my-macbook.tailnet.ts.net:3100
 If you access Paperclip with a custom private hostname, add it to the allowlist:
 
 ```sh
-pnpm paperclipai allowed-hostname my-macbook.tailnet.ts.net
+pnpm exec paperclipai allowed-hostname my-macbook.tailnet.ts.net
 ```
 
 ## 5. Verify the server is reachable