feat(psf): transition to Order 2 (Sovereign Architect) with advanced skill graph and philosophical alignment

notes/org-skill-scientist.org

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+#+TITLE: SKILL: The Scientist Agent (Universal Literate Note)
+#+ID: skill-scientist
+#+STARTUP: content
+#+FILETAGS: :debugging:science:logic:tdd:psf:
+#+DEPENDS_ON: skill-tdd-runner skill-scribe-rca
+
+* Overview
+The **Scientist Agent** provides a formal, hypothesis-driven approach to debugging. Instead of "trial and error," it formulates symbolic theories about why a failure occurred, designs experiments (test cases), and updates the system's **Institutional Memory** upon discovery.
+
+* Phase A: Demand (PRD)
+:PROPERTIES:
+:STATUS: FROZEN
+:END:
+
+** 1. Purpose
+Eliminate speculative debugging through rigorous scientific methodology.
+
+** 2. User Needs
+- **Hypothesis Formulation:** Neural generation of potential failure causes.
+- **Experimental Design:** Autonomous creation of minimal failing test cases.
+- **Theory Verification:** Execution of tests via the TDD Runner.
+- **Knowledge Update:** Permanent update to `RCA.org` to prevent regression.
+
+* Phase D: Build (Implementation)
+
+** Scientific Loop
+#+begin_src lisp :tangle projects/org-skill-scientist/src/scientist-logic.lisp
+(defun scientist-formulate-hypothesis (failure-log)
+  "Analyzes an error and proposes a 'Theory of Failure'."
+  (org-agent:ask-neuro 
+   (format nil "Explain why this failure occurred and propose a specific experiment to prove it: ~a" failure-log)
+   :system-prompt "You are a PSF Senior Debugging Scientist. Use formal logic and the scientific method."))
+
+(defun scientist-run-experiment (hypothesis)
+  "Designs a minimal test case based on a hypothesis."
+  ;; Delegates to TDD Runner to create and run the experiment.
+  (org-agent:spawn-task (format nil "Create a minimal failing test for: ~a" hypothesis)))
+#+end_src
+
+* Registration
+#+begin_src lisp
+(defskill :skill-scientist
+  :priority 90
+  :trigger (lambda (context) (search "ERROR" (getf (getf context :payload) :text)))
+  :neuro #'scientist-formulate-hypothesis
+  :symbolic (lambda (action context) action))
+#+end_src