docs: close out Scient rename

AGENTS.md

@@ -3,28 +3,27 @@
 Status: Active
 Owner: Yaacov
 Last updated: 2026-07-17
-Purpose: Defines how agents should work in this early PapiLab repository.
+Purpose: Defines how agents should work in this early Scient repository.
 Doc type: Agent protocol
 
 ## What This Repo Is
 
-This repo is the early planning and documentation workspace for PapiLab.
+This repo is the early planning and documentation workspace for Scient.
 
-PapiLab is a local-first, cloud-mirrored scientific workspace where researchers and AI agents run an entire research project together, from research question to publication-ready manuscript. The product direction is still being shaped.
+Scient is a local-first, cloud-mirrored scientific workspace where researchers and AI agents run an entire research project together, from research question to publication-ready manuscript. The product direction is still being shaped.
 
 ## Current State
 
 This parent repo remains documentation-first. The maintained desktop fork now
-contains the first permanent PapiLab-owned package, `@papilab/project-init`,
+contains the first permanent Scient-owned package, `@scientfactory/project-init`,
 but the broader application architecture and first scientific vertical slice
 have not been built. Do not infer scientific-state, gateway, sync, cloud, or
 production boundaries from that narrow package.
 
-ScientFactory is the chosen future company identity. **Scient** is the chosen
-public name for both the future application and its native first-party research
-agent. The current implemented application identity remains PapiLab until the
-rename plan is executed and verified. In technical contexts, use **Scient app**
-and **Scient agent** whenever the meaning could be ambiguous.
+ScientFactory is the company and GitHub organization identity. **Scient** is
+the public name for both the implemented application and its planned native
+first-party research agent. In technical contexts, use **Scient app** and
+**Scient agent** whenever the meaning could be ambiguous.
 
 The Scient agent is planned but not yet implemented. Architecturally, it is the
 owned OpenCode-derived agent itself—not an app shell around a separate OpenCode
@@ -47,7 +46,7 @@ Capture durable future context, not documentation volume. Preserve consequential
 
 AI may draft documentation, but it is not the accountable owner and cannot confer acceptance. Preserve uncertainty and specific reasoning for human review. When authoritative sources conflict, surface the contradiction and route it to the owning person or document instead of smoothing it into false agreement.
 
-Keep this repository within its PapiLab product and project boundary. Do not add company-wide finance, legal, people, customer-record, or cross-product authority here without an accepted repository-scope decision. Do not commit secrets or sensitive personal, customer, employee, or regulated data.
+Keep this repository within its Scient product and project boundary. Do not add company-wide finance, legal, people, customer-record, or cross-product authority here without an accepted repository-scope decision. Do not commit secrets or sensitive personal, customer, employee, or regulated data.
 
 ## Source Documents
 
@@ -56,14 +55,14 @@ Current important documents:
 - `docs/README.md` - documentation map and current repo structure.
 - `docs/documentation-policy.md` - rules for creating, updating, and classifying documentation.
 - `docs/product/PRD.md` - product direction, core capabilities, user experience principles, and technical requirements.
-- `docs/product/scient-product-identity.md` - accepted future company, application, agent, external-agent, and naming vocabulary.
+- `docs/product/scient-product-identity.md` - accepted company, application, agent, external-agent, and naming vocabulary.
 - `docs/product/product-philosophy.md` - durable product principles that guide product, architecture, design, quality, and implementation.
 - `docs/architecture/technology-stack.md` - current technology stack direction and open implementation decisions.
-- `docs/architecture/decisions/ADR-0001-synara-opencode-foundation-and-papilab-ownership-boundary.md` - accepted initial application/runtime foundations and the PapiLab-owned scientific boundary.
+- `docs/architecture/decisions/ADR-0001-synara-opencode-foundation-and-scient-ownership-boundary.md` - accepted initial application/runtime foundations and the Scient-owned scientific boundary.
 - `docs/planning/product-roadmap.md` - active sequence of coherent product outcomes.
-- `docs/planning/first-papilab-vertical-slice-implementation-plan.md` - concrete plan and acceptance criteria for the current implementation slice.
+- `docs/planning/first-scient-vertical-slice-implementation-plan.md` - concrete plan and acceptance criteria for the current implementation slice.
 - `docs/planning/scient-and-external-agents-implementation-plan.md` - proposed implementation plan for the Scient agent, external-agent preservation, and Scient-versus-external-agent identity isolation.
-- `docs/planning/papilab-to-scient-rename-execution-plan.md` - proposed migration plan from the current PapiLab implementation identity to Scient and ScientFactory.
+- `docs/planning/papilab-to-scient-rename-execution-plan.md` - historical execution and rollback record for the PapiLab-to-Scient migration.
 
 Use each document according to its metadata. The PRD and ADR-0001 are accepted
 direction; the roadmap is active planning; the product philosophy, technology
@@ -90,7 +89,7 @@ When proposing technical direction, separate:
 
 The PRD should stay focused on product truth. Stack choices and implementation details should live in architecture documents unless they are direct product constraints.
 
-Use **Scient** as the public name for both the future app and native agent. In
+Use **Scient** as the public name for both the app and native agent. In
 technical or potentially ambiguous text, write **Scient app** or **Scient
 agent**. Use **external agent** for an independently connected product such as
 OpenCode, Codex, Claude, or Droid. Do not create “ScientApp” or “ScientAgent” as
@@ -102,9 +101,9 @@ are project instructions, not the Scient agent product.
 
 Project-specific skills live under `skills/`.
 
-Use `skills/product/papilab-product-stewardship/SKILL.md` for product management work, including PRD changes, feature analysis, roadmap notes, product decisions, and product research synthesis.
+Use `skills/product/scient-product-stewardship/SKILL.md` for product management work, including PRD changes, feature analysis, roadmap notes, product decisions, and product research synthesis.
 
-Use `skills/documentation/papilab-documentation-stewardship/SKILL.md` when creating, reviewing, moving, promoting, retiring, or reconciling durable documentation and project progress records.
+Use `skills/documentation/scient-documentation-stewardship/SKILL.md` when creating, reviewing, moving, promoting, retiring, or reconciling durable documentation and project progress records.
 
 Project skills are workflow helpers. They should point agents back to the canonical repo documents and must not override `docs/product/`, `docs/architecture/`, `docs/documentation-policy.md`, or this `AGENTS.md` file.
 

README.md

@@ -1,23 +1,23 @@
-# PapiLab
+# Scient
 
 Status: Active
 Owner: Yaacov
 Last updated: 2026-07-17
-Purpose: Entry point for the PapiLab planning repository.
+Purpose: Entry point for the Scient planning repository.
 Doc type: Repo orientation
 
-PapiLab remains the current repository and implemented desktop identity. The
+Scient is the current repository and implemented desktop identity. The
 repository is documentation-first, with one narrow project-initiation package
-in the maintained desktop fork. ScientFactory and Scient are the accepted
-future identity, but the rename has not yet been executed.
+in the maintained desktop fork. The native Scient agent remains planned; its
+owned source repository is `ScientFactory/scient-agent`.
 
 Start here:
 
 - [Collaborator onboarding](docs/onboarding.md) - read this first for the project journey, repository tour, and role-specific reading paths.
 - [Documentation index](docs/README.md) - map of the repository's documentation areas.
 - [Documentation policy](docs/documentation-policy.md) - rules for document authority, status, evidence, and placement.
 - [Product requirements](docs/product/PRD.md) - accepted product direction.
-- [Scient product identity](docs/product/scient-product-identity.md) - accepted future company, app, native-agent, and external-agent naming system.
-- [PapiLab-to-Scient rename plan](docs/planning/papilab-to-scient-rename-execution-plan.md) - proposed controlled migration; target names are not yet implemented.
+- [Scient product identity](docs/product/scient-product-identity.md) - accepted company, app, native-agent, and external-agent naming system.
+- [PapiLab-to-Scient rename record](docs/planning/papilab-to-scient-rename-execution-plan.md) - historical migration, compatibility, rollback, and deferred-public-cutover record.
 - [Technology stack](docs/architecture/technology-stack.md) - proposed architecture and stack direction.
 - [Agent guidance](AGENTS.md) - protocol for agents working in this repository.

docs/README.md

@@ -3,11 +3,11 @@
 Status: Active
 Owner: Yaacov
 Last updated: 2026-07-17
-Purpose: Maps the PapiLab documentation structure and where each kind of information belongs.
+Purpose: Maps the Scient documentation structure and where each kind of information belongs.
 Doc type: Repo orientation
 
 This parent repository remains documentation-first. The maintained desktop fork
-contains the first narrow PapiLab-owned project-initiation package, while the
+contains the first narrow Scient-owned project-initiation package, while the
 scientific application architecture and vertical slice remain unbuilt. This
 structure gives product, architecture, planning, research, development, and
 operations material clear homes without presenting planned behavior as current
@@ -20,13 +20,13 @@ Start here:
 - [Collaborator onboarding](onboarding.md) - ordered project journey, repository tour, and contribution-area reading routes.
 - [Documentation policy](documentation-policy.md) - documentation rules, metadata, statuses, and placement policy.
 - [Product requirements](product/PRD.md) - canonical product direction.
-- [Scient product identity](product/scient-product-identity.md) - accepted future company, app, native-agent, external-agent, and naming vocabulary.
+- [Scient product identity](product/scient-product-identity.md) - accepted company, app, native-agent, external-agent, and naming vocabulary.
 - [Product philosophy](product/product-philosophy.md) - draft durable product principles; the accepted PRD governs conflicts.
 - [Technology stack](architecture/technology-stack.md) - current proposed stack direction.
 - [Product roadmap](planning/product-roadmap.md) - current sequence of coherent product outcomes.
-- [First vertical-slice implementation plan](planning/first-papilab-vertical-slice-implementation-plan.md) - bounded plan for the active product slice.
+- [First vertical-slice implementation plan](planning/first-scient-vertical-slice-implementation-plan.md) - bounded plan for the active product slice.
 - [Scient and external agents implementation plan](planning/scient-and-external-agents-implementation-plan.md) - proposed plan for building the Scient agent as the owned OpenCode-derived first-party agent while preserving external agents independently.
-- [PapiLab-to-Scient rename execution plan](planning/papilab-to-scient-rename-execution-plan.md) - proposed controlled migration from the current PapiLab implementation identity to Scient and ScientFactory.
+- [PapiLab-to-Scient rename execution record](planning/papilab-to-scient-rename-execution-plan.md) - historical migration, compatibility, rollback, and deferred-public-cutover record.
 - [LitRev-to-PapiLab rename execution plan](planning/litrev-to-papilab-rename-execution-plan.md) - historical intermediate identity migration, verification, and rollback record.
 - [Architecture](architecture/README.md) - architecture direction, future architecture homes, and decisions.
 - [Design](design/README.md) - future home for product design principles and UI guidance.

docs/architecture/README.md

@@ -3,17 +3,17 @@
 Status: Active
 Owner: Yaacov
 Last updated: 2026-07-17
-Purpose: Defines where PapiLab architecture direction, future architecture homes, and decisions belong.
+Purpose: Defines where Scient architecture direction, future architecture homes, and decisions belong.
 Doc type: Repo orientation
 
-Architecture docs explain how PapiLab should be structured and why. They must clearly distinguish proposal, accepted direction, implementation candidate, and current implementation.
+Architecture docs explain how Scient should be structured and why. They must clearly distinguish proposal, accepted direction, implementation candidate, and current implementation.
 
 Current documents:
 
 - `technology-stack.md` - current stack direction.
-- `project-format.md` - future home for the PapiLab project format.
+- `project-format.md` - future home for the Scient project format.
 - `local-first-sync.md` - future home for local-first and sync architecture.
 - `collaboration-model.md` - future home for collaboration architecture.
 - `agent-runtime.md` - future home for detailed Scient and external-agent runtime architecture; the accepted high-level ownership boundary currently lives in ADR-0001.
 - `security-and-permissions.md` - early security, trust-boundary, and permission principles.
-- `decisions/` - accepted architecture decision records, beginning with the Synara application foundation, Scient's OpenCode-derived source foundation, external-agent separation, and the PapiLab-owned scientific boundary.
+- `decisions/` - accepted architecture decision records, beginning with the Synara application foundation, Scient's OpenCode-derived source foundation, external-agent separation, and the Scient-owned scientific boundary.

docs/architecture/agent-runtime.md

@@ -6,10 +6,10 @@ Last updated: 2026-07-17
 Purpose: Defines what should be documented about Scient-agent and external-agent execution once implementation begins.
 Doc type: Future home
 
-This page will document PapiLab's agent runtime architecture when it exists.
+This page will document Scient's agent runtime architecture when it exists.
 
 The accepted high-level foundation and ownership boundary currently lives in
-`decisions/ADR-0001-synara-opencode-foundation-and-papilab-ownership-boundary.md`.
+`decisions/ADR-0001-synara-opencode-foundation-and-scient-ownership-boundary.md`.
 The proposed implementation sequence and identity-isolation requirements live
 in `../planning/scient-and-external-agents-implementation-plan.md`.
 This file remains a placeholder until the first vertical slice validates a

docs/architecture/collaboration-model.md

@@ -2,11 +2,11 @@
 
 Status: Placeholder
 Owner: Yaacov
-Last updated: 2026-06-27
+Last updated: 2026-07-17
 Purpose: Defines what should be documented about sharing and collaboration once the model is designed.
 Doc type: Future home
 
-This page will document PapiLab's collaboration model when it exists.
+This page will document Scient's collaboration model when it exists.
 
 Document here: