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## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - The CLI exposes board/operator controls for managing agent configuration and instructions. > - Agent instructions files influence future agent behavior, so deleting one is a destructive configuration mutation. > - Nearby destructive CLI commands already require explicit `--yes` confirmation before sending DELETE requests. > - `agent instructions-file:delete` skipped that local confirmation guard and could delete a bundle file from a scripted or mistyped command. > - This pull request aligns that command with the existing destructive-command safety convention. > - The benefit is a small, predictable operator-safety guard with focused regression coverage. ## Linked Issues or Issue Description Bug report: ### Pre-submission checklist - [x] I have searched existing open and closed issues and this is not a duplicate. - [x] I am on the latest released version of Paperclip (or can reproduce on `master`). - [x] I have confirmed the error originates in Paperclip itself — not in my agent adapter, API provider, or local configuration. ### What happened? `paperclipai agent instructions-file:delete` deleted an agent instructions bundle file without requiring explicit CLI confirmation. ### Expected behavior Destructive CLI delete operations should require `--yes` before sending a DELETE request. ### Steps to reproduce 1. Run `npx paperclipai agent instructions-file:delete <agent-id> --path AGENTS.md`. 2. Observe that the CLI immediately issues `DELETE /api/agents/:agentId/instructions-bundle/file?path=AGENTS.md`. 3. No local confirmation guard blocks the destructive request. ### Paperclip version or commit `fd472d02ba950519ca5eff75ed9fd55cf976f4c2` ### Deployment mode Local dev (`pnpm dev`) ### Installation method Built from source (`pnpm dev` / `pnpm build`) ### Agent adapter(s) involved - [x] Not adapter-specific (core bug) ### Database mode Not database-related ### Access context Board (human operator) ### Node.js version `v20.x` ### Operating system macOS ### Relevant logs or output ```text Current behavior is local CLI behavior: the command proceeds to the DELETE call without requiring `--yes`. ``` ### Relevant config (if applicable) None. ### Additional context This command already sits next to other destructive CLI actions such as `agent delete`, which require explicit confirmation. Aligning the guard makes the CLI safety model consistent. ### Privacy checklist - [x] I have reviewed all pasted output for PII (usernames, file paths, API keys, tokens, company names) and redacted where necessary. ## What Changed - Added a `--yes` confirmation option to `agent instructions-file:delete`. - Refuse the command locally before resolving API context or sending a DELETE request when confirmation is missing. - Updated CLI parity coverage for confirmed and refused instructions-file deletion. - Updated the CLI documentation example to include `--yes`. ## Verification - `/Users/xinran/Downloads/dev/paperclip-pr-work/node_modules/.bin/vitest run cli/src/__tests__/agent-lifecycle.test.ts --config cli/vitest.config.ts` equivalent executed from the PR worktree using temporary dependency symlinks: 3 tests passed. - `git diff --check` ## Risks - Low risk: this only changes one destructive CLI command and matches existing `agent delete`, `issue delete`, and other delete-command confirmation behavior. - Scripts that intentionally delete instructions files must add `--yes`, which is the intended explicit confirmation path. - No database, API contract, or lockfile changes. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - OpenAI Codex, GPT-5-based coding agent in Codex desktop with shell/tool use and local test execution. ## 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 - [ ] All Paperclip CI gates are green - [ ] 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: 馨冉 <xinxincui239@gmail.com> Co-authored-by: Paperclip <noreply@paperclip.ing>