## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - The CLI and server both update Paperclip values in `.env` files
> - The server preserved operator content, but the CLI rebuilt the
complete file
> - A CLI rerun could remove comments, custom values, ordering, and
newline style
> - Both paths need one editor with one value encoding and duplicate key
policy
> - The final integration also needs one regression test across the
related setup and sync safety mechanisms
> - This pull request moves the editor to the shared package and adds
cross-cutting rerun-survival coverage
> - The benefit is safe setup and worktree repair reruns that preserve
operator edits
## Linked Issues or Issue Description
**What happened?**
The CLI rebuilt the complete `.env` file when it wrote a managed
Paperclip value. This action removed comments, blank lines, custom keys,
original quoting, and the original newline style.
**Expected behavior**
Paperclip must update only the managed assignments. It must preserve all
unrelated bytes. It must skip the file replacement when all managed
values are current.
**Steps to reproduce**
1. Add comments, custom keys, quoted values, and CRLF newlines to the
Paperclip `.env` file.
2. Run a CLI path that calls the agent JWT secret setup.
3. Observe that the old writer replaces the complete file.
**Paperclip version or commit**
The problem exists on `master` before this pull request.
Related public context: Refs #437.
## What Changed
- Add one shared line-preserving `.env` editor for the CLI and server.
- Define minimal and JSON value encodings in the shared helper.
- Update every stale duplicate of a managed key and preserve current
duplicate encodings.
- Preserve comments, ordering, blank lines, unknown keys, export
prefixes, trailing comments, and newline style.
- Write changed files through a same-directory temporary file and atomic
rename.
- Limit CLI updates to non-empty `PAPERCLIP_*` entries.
- Skip the write when all managed values are current.
- Add shared, CLI, and server regression coverage.
- Refresh the branch after the related config, sandbox, and skill safety
changes landed.
- Add a cross-cutting integration test for config, env-file,
managed-sandbox, and managed-instructions rerun survival.
## Verification
- `pnpm exec vitest run packages/shared/src/env-file.test.ts
packages/shared/src/config-schema.test.ts
cli/src/__tests__/agent-jwt-env.test.ts
cli/src/__tests__/config-store.test.ts
server/src/__tests__/config-file.test.ts
server/src/__tests__/worktree-config.test.ts` passes 39 tests.
- `pnpm exec vitest run
server/src/__tests__/rerun-survival.integration.test.ts` passes 4 tests.
- `pnpm -r typecheck` passes on the previous head. GitHub CI reruns it
on the refreshed head.
- The previous head passed the complete general, serialized, workspace,
and E2E matrix. GitHub CI reruns that matrix on the refreshed head.
- `pnpm build` passes on the previous head. GitHub CI reruns it on the
refreshed head.
## Risks
- Low risk. The production change only affects managed `.env`
assignments.
- Existing managed assignments can keep their original quoting when
their decoded values are current.
- Changed CLI values keep the prior minimal encoding policy. Changed
server values keep the prior JSON encoding policy.
- Duplicate managed assignments now follow one explicit rule: Paperclip
updates each stale occurrence.
- The master refresh had one import-block conflict. The resolution keeps
both the config merge imports and the env-file imports.
- The added integration file is test-only. It has no database, API, or
UI contract effect.
> 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 from the GPT-5 family produced this change with reasoning,
tool use, and code execution. The runtime did not expose the exact model
ID or context window size.
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The CLI and server share a JSON configuration contract for local
installations and worktrees.
> - Existing config writes removed extension keys because Zod stripped
unknown object properties.
> - Invalid config files could also be replaced with defaults before an
operator preserved the original bytes.
> - Configuration updates must preserve operator edits and must not
rewrite files when the effective value is unchanged.
> - This pull request adds extension-preserving merges, guarded
invalid-config repair, atomic writes, and focused regression tests.
> - The benefit is safe setup and configuration reruns without data loss
or unnecessary mtime changes.
## Linked Issues or Issue Description
**What happened?**
Known-field updates through the CLI or server removed unknown top-level
and nested config keys. Non-interactive configure and onboard paths
could replace a present but invalid config with defaults.
**Expected behavior**
Writers preserve extension keys, skip semantic no-op writes, and require
explicit interactive confirmation before an invalid config is replaced.
Repair preserves an exact collision-safe backup first.
**Steps to reproduce**
1. Add an unknown top-level key and an unknown nested provider key to
`config.json`.
2. Update a known field through the CLI or worktree config writer.
3. Observe that the extension keys are removed on the base branch.
4. Write invalid JSON and run configure or onboard without an
interactive terminal.
5. Observe that the original file can be replaced without a durable
invalid-file backup on the base branch.
**Paperclip version or commit**
`master` at the pull request base commit.
## What Changed
- Accept unknown properties at each extensible config object boundary
while keeping every known field validated.
- Merge known-field updates into the parsed source config and preserve
only unknown extension data.
- Warn about near-match key names without deleting or changing them.
- Skip writes when the effective config is unchanged, which keeps file
mtimes stable.
- Write config changes through a temporary file, file sync, rename, and
directory sync.
- Distinguish a missing config from an invalid config in configure and
onboard.
- Back up invalid bytes as `config.json.invalid-N` and verify the source
still matches that backup before repair.
- Require interactive repair confirmation and reject non-interactive
replacement with an actionable message.
- Document the config preservation and repair behavior.
## Verification
- `pnpm exec vitest run packages/shared/src/config-schema.test.ts
cli/src/__tests__/config-store.test.ts
cli/src/__tests__/configure-repair.test.ts
cli/src/__tests__/configure.test.ts cli/src/__tests__/onboard.test.ts
server/src/__tests__/config-file.test.ts
server/src/__tests__/worktree-config.test.ts`
- `pnpm -r typecheck`
- `AWS_ACCESS_KEY_ID= AWS_SECRET_ACCESS_KEY= VITEST_MAX_WORKERS=1 pnpm
test:run`
- `pnpm build`
- Confirm all pull request checks are green on the latest commit.
- Confirm Greptile reports 5/5 with no unresolved comments.
## Risks
- Passthrough keeps misspelled keys. Near-match warnings make this
visible without destructive cleanup.
- Merge behavior must distinguish unknown extension keys from optional
known keys. Schema-aware regression tests cover preservation and
known-key deletion.
- Repair must not overwrite bytes that changed after backup. The writer
compares the current source with the selected backup before atomic
replacement.
- The change does not alter database schema, company scoping, or
activity logging.
> 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 model family. The exact deployment model ID and
context window are not exposed. Agentic reasoning, tool use, and code
execution were enabled.
## 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>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system needs host contracts and runtime support before
large plugins can integrate cleanly.
> - The source branch mixed the LLM Wiki package with supporting
host/runtime work, managed plugin skills, root-level storage spaces, and
a bookmarks reference plugin.
> - [PAP-9173](/PAP/issues/PAP-9173) asked for the current branch to be
split by file boundary: plugin package separately from everything else.
> - [PAP-9188](/PAP/issues/PAP-9188) clarified that LLM Wiki may have
plugin-local spaces, but Paperclip core should not reorganize top-level
local storage into spaces.
> - Follow-up review clarified that the bookmarks example should not
ship in this PR either.
> - This pull request contains the
non-`packages/plugins/plugin-llm-wiki/` host/runtime work, keeps runtime
state under the selected Paperclip instance root, and no longer includes
the bookmarks example.
## What Changed
- Added/updated plugin host contracts, SDK types, worker RPC plumbing,
managed plugin skill support, and related server tests.
- Removed the bookmarks example plugin package and its
bundled-example/workspace references.
- Removed the root-level local spaces CLI/migration surface and restored
instance-root runtime defaults for config, db, logs, storage, secrets,
workspaces, projects, and adapter homes.
- Replaced shared root `space-paths` helpers with `home-paths` helpers
for core runtime storage.
- Tightened stranded recovery unique-conflict detection so concurrent
recovery scans reuse the raced recovery issue when Postgres errors are
wrapped.
- Kept `packages/plugins/plugin-llm-wiki/` out of this PR diff;
plugin-local spaces remain in the stacked plugin-only PR.
## Verification
- `pnpm exec vitest run cli/src/__tests__/data-dir.test.ts
cli/src/__tests__/home-paths.test.ts cli/src/__tests__/onboard.test.ts
packages/shared/src/home-paths.test.ts
packages/db/src/runtime-config.test.ts
server/src/__tests__/agent-instructions-service.test.ts
server/src/__tests__/claude-local-execute.test.ts
server/src/__tests__/codex-local-execute.test.ts`
- `pnpm exec vitest run packages/db/src/runtime-config.test.ts`
- `pnpm exec vitest run
server/src/__tests__/plugin-routes-authz.test.ts`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "reuses the
raced stranded recovery issue"` skipped locally because embedded
Postgres did not initialize on this macOS temp host; the code path was
typechecked and is covered by Linux CI.
- Boundary check: no core references remain for `PAPERCLIP_SPACE_ID`,
`spaces migrate-default`, `@paperclipai/shared/space-paths`,
`registerSpacesCommands`, or the removed bookmarks example.
- Previous PR head `4f23e034` had green GitHub checks: `verify`, all
four serialized server shards, `e2e`, `Canary Dry Run`, `policy`, Snyk,
and `Greptile Review`. Current head `582f466d` is re-running checks
after the bookmarks deletion.
## Risks
- Plugin host changes touch shared runtime paths, so regressions would
most likely appear in adapter startup, plugin loading, or local dev path
defaults.
- Removing the bookmarks example also removes one demonstration of
plugin database namespaces plus local-folder persistence; remaining
plugin examples still cover bundled example discovery and plugin host
flows.
- The plugin package itself is intentionally deferred to the stacked
plugin-only PR, where LLM Wiki plugin-local spaces live.
- Existing installs that tested the transient root-level spaces CLI
should stop using it; this PR intentionally removes that unsupported
migration surface before merge.
> 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 GPT-5 Codex via Codex CLI, tool use and local code execution
enabled; context window not exposed.
## 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 run tests locally and they pass, except where noted above
for host-specific embedded Postgres initialization
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
Stacked follow-up: PR #5592 contains only
`packages/plugins/plugin-llm-wiki/` and targets this branch.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
Rename all workspace packages from @paperclip/* to @paperclipai/* and
the CLI binary from `paperclip` to `paperclipai` in preparation for
npm publishing. Bump CLI version to 0.1.0 and add package metadata
(description, keywords, license, repository, files). Update all
imports, documentation, user-facing messages, and tests accordingly.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add --data-dir option to all CLI commands, allowing users to override
the default ~/.paperclip root for config, context, database, logs, and
storage. Includes preAction hook to auto-derive --config and --context
paths when --data-dir is set. Add unit tests and doc updates.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Reject requests from unrecognised Host headers when running
authenticated/private. Adds server middleware, CLI `allowed-hostname`
command, config-schema field, and prompt support for configuring
allowed hostnames during onboard/configure.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Extend server setup prompts with deployment mode (local_trusted vs
authenticated), exposure (private vs public), bind host, and auth config.
Add auth bootstrap-ceo command that creates a one-time invite URL for the
initial instance admin. Add deployment-auth-check to doctor diagnostics.
Register the new command in the CLI entry point.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Introduces a provider-agnostic storage subsystem for file attachments.
Includes local disk and S3 backends, asset/attachment DB schemas, issue
attachment CRUD routes with multer upload, CLI configure/doctor/env
integration, and enriched issue ancestors with project/goal resolution.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add ensureLocalSecretsKeyFile helper that generates a random 32-byte
master key during onboard if using local_encrypted provider. Move
resolveRuntimeLikePath to cli/src/utils/ for reuse by secrets-key
and existing check modules.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add secrets section to onboard, configure, and doctor commands. Doctor
validates local encrypted provider key file and can auto-repair missing
keys. Extract shared path resolution into path-resolver module used by
database and log checks. Show secrets env vars in `paperclip env`.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add HS256 JWT-based authentication for local adapters (claude_local, codex_local)
so agents authenticate automatically without manual API key configuration. The
server mints short-lived JWTs per heartbeat run and injects them as PAPERCLIP_API_KEY.
The auth middleware verifies JWTs alongside existing static API keys.
Includes: CLI onboard/doctor JWT secret management, env command for deployment,
config path resolution from ancestor directories, dotenv loading on server startup,
event payload secret redaction, multi-status issue filtering, and adapter transcript
parsing for thinking/user message kinds.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Rework config store with better file handling. Expand heartbeat-run
command with richer output and error reporting. Improve configure
and onboard commands. Update doctor checks.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add cli/ package with initial scaffolding. Add config-schema to shared
package for typed configuration. Add server config-file loader for
paperclip.config.ts support. Register cli in pnpm workspace. Add
.paperclip/ and .pnpm-store/ to gitignore. Minor Companies page fix.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Dotta
Dotta
dotta
Forgotten