Run loop: document scientist-focused README differentiation

Author: drpedapati

manuscript/sciclaw-component-revision-plan.qmd

@@ -317,6 +317,22 @@ Use a layered naming strategy instead of hard renames:
   - `make build`
 - Upstream synchronization in this loop merged substantial additional updates (Docker, docs, provider changes), and compatibility checks remained green post-merge.
 
+## Commit Slice F: Scientist-Facing README Rebranding and Diff Guidance
+
+- Updated `README.md` with a dedicated section describing:
+  - sciClaw's scientific use-case positioning,
+  - concrete differences from stock PicoClaw,
+  - compatibility boundaries kept intact (CLI command and upstream sync model).
+- Added an explicit comparison table for scientists covering:
+  - workspace defaults,
+  - runtime prompt semantics,
+  - migration behavior,
+  - CLI branding behavior,
+  - manuscript/reproducibility workflow expectations.
+- Validation executed:
+  - `go test ./cmd/picoclaw ./pkg/migrate ./pkg/agent`
+  - `make build`
+
 # Phased Revision Plan
 
 ## Phase 1: Stabilize Baseline

manuscript/sciclaw-manuscript-outline.qmd

@@ -86,6 +86,7 @@ See @fig-system-architecture.
 - Runtime paired-scientist semantics are now implemented in core prompt/context construction, including reproducibility-focused system rules and `TOOLS.md` bootstrap context loading with test coverage.
 - Workspace migration logic is now aligned with paired-scientist defaults by migrating `IDENTITY.md`, `sessions/`, and `cron/`, with dedicated migration test coverage.
 - CLI display surfaces now present sciClaw branding while preserving `picoclaw` command compatibility, with dedicated output tests and successful post-merge validation.
+- README now includes a scientist-focused stock-vs-sciClaw diff section so research users can quickly understand behavioral, reproducibility, and workflow deltas.
 
 # Methods {#sec-methods}
 

plans/main-plan-activity.md

@@ -22,3 +22,5 @@
 - Timestamp: 2026-02-12T14:52:32Z | Git hash: fc4a501
 - Continued implementation with strategic commits: rebranded CLI display surfaces to sciClaw with explicit `picoclaw` compatibility messaging, added CLI branding tests, merged latest upstream changes, reran build/tests, updated manuscript implementation status, and re-rendered manuscript outputs.
 - Timestamp: 2026-02-12T17:01:59Z | Git hash: a7554fe
+- Continued implementation with strategic commits: updated README with a scientist-specific stock-vs-sciClaw comparison and explicit rebranding/compatibility guidance, reran build/tests, updated manuscript implementation status, and re-rendered manuscript outputs.
+- Timestamp: 2026-02-12T18:00:30Z | Git hash: 44c174f

plans/main-plan-log.csv

@@ -11,3 +11,4 @@ timestamp,loop,action,status,git_hash,notes
 2026-02-12T14:49:13Z,10,"Continued implementation with runtime prompt/context strategic slice",completed,bd8a306,"Implemented sciClaw runtime identity and reproducibility rules in pkg/agent/context.go, loaded TOOLS.md bootstrap context, added pkg/agent context tests, upstream sync no-op, build/tests passed, rendered manuscript outputs"
 2026-02-12T14:52:32Z,11,"Continued implementation with workspace migration alignment slice",completed,fc4a501,"Extended migration scope for IDENTITY.md and sessions/cron directories, expanded migrate tests, merged upstream/main, build/tests passed, updated manuscript implementation status, rendered manuscript outputs"
 2026-02-12T17:01:59Z,12,"Continued implementation with CLI display rebranding slice",completed,a7554fe,"Rebranded CLI user-facing output to sciClaw while preserving picoclaw command compatibility, added CLI branding tests, merged upstream/main with large Docker/docs/provider updates, build/tests passed, updated manuscript implementation status, rendered manuscript outputs"
+2026-02-12T18:00:30Z,13,"Continued implementation with scientist-facing README differentiation slice",completed,44c174f,"Added specific stock PicoClaw vs sciClaw comparison and scientist-oriented use-case guidance to README, tests/build passed, updated manuscript implementation status, rendered manuscript outputs"

plans/main-plan.md

@@ -61,6 +61,8 @@ do deep review of the plan including thinking about high level vision, peer revi
 
 Now start implementing the plan with strategic commits and build tests all the way through
 
+update readme for new branding and use case with description on what's changed from original. be specific to help scientists undrfstand the differences between stock picoclaw and our revision. 
+
 ### One-Time Instructions — Tasks that should only execute once
 
 <!-- 👤 AUTHOR AREA: Add one-time tasks below -->