chore: structural cleanup of projects and patches

projects/org-skill-web-research/projectsorg-skill-web-research/tests/test-suite.lisp

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+;;; TDD Suite for web-research
+;;; TDD Suite for web-research\n(fiveam:test mock-test (5am:is t))

projects/org-skill-workspace-manager/projectsorg-skill-workspace-manager/tests/test-suite.lisp

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+;;; TDD Suite for workspace-manager
+;;; TDD Suite for workspace-manager\n(fiveam:test mock-test (5am:is t))

system/patches/patch-architect-actuate.lisp

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+(in-package :org-agent.skills.org-skill-architect)
+
+(defun architect-actuate (action context)
+  (declare (ignore context))
+  (let* ((payload (getf action :payload))
+         ;; Support both (getf action :payload) and direct top-level keys
+         (note-path (or (getf payload :path) (getf action :path)))
+         (blueprint-content (or (getf payload :content) (getf action :content))))
+    
+    (if (and note-path blueprint-content)
+        (progn
+          (org-agent:kernel-log "ARCHITECT - Appending PROTOCOL to ~a" note-path)
+          (with-open-file (out note-path :direction :output :if-exists :append)
+            (format out "~%* Phase B: Blueprint (PROTOCOL)~%:PROPERTIES:~%:STATUS: SIGNED~%:END:~%~%~a" 
+                    blueprint-content))
+          (format nil "SUCCESS - Architect established PROTOCOL in ~a" note-path))
+        (progn
+          (org-agent:kernel-log "ARCHITECT FAILURE - Missing path or content in action: ~a" action)
+          nil))))

system/patches/patch-architect-neuro.lisp

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+(in-package :org-agent.skills.org-skill-architect)
+
+(defun neuro-skill-architect (context)
+  (let* ((payload (getf context :payload))
+         (note (car (getf payload :ready-notes)))
+         (note-path (getf note :note-path))
+         (prd-content (getf note :content))
+         (path-str (namestring note-path)))
+    (format nil "
+      You are the PSF Architect. 
+      The Master Note '~a' has a FROZEN PRD and needs a PROTOCOL. 
+      
+      NOTE CONTENT:
+      ---
+      ~a
+      ---
+      
+      TASK:
+      Draft the '* Phase B: Blueprint (PROTOCOL)' section.
+      1. Define Architectural Intent.
+      2. Define Semantic Interfaces using Lisp signatures.
+      
+      Return a Lisp plist: (:target :architect :action :actuate :path \"~a\" :content \"...blueprint section...\")
+    " path-str prd-content path-str)))

system/patches/patch-architect-scan.lisp

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+(in-package :org-agent.skills.org-skill-architect)
+
+(defun architect-scan-all-notes ()
+  (let* ((notes-dir (or (uiop:getenv "MEMEX_NOTES") "/home/user/memex/notes/"))
+         (files (uiop:directory-files (uiop:ensure-directory-pathname notes-dir)))
+         (ready-notes '()))
+    (org-agent:kernel-log "ARCHITECT - Scanning ~a files in ~a" (length files) notes-dir)
+    (dolist (file files)
+      (let ((name (pathname-name file))
+            (type (pathname-type file)))
+        (when (and name type 
+                   (uiop:string-prefix-p "org-skill-" name)
+                   (string-equal type "org"))
+          (let ((status (architect-perceive-frozen-prd file)))
+            (when status (push status ready-notes))))))
+    (org-agent:kernel-log "ARCHITECT - Found ~a ready notes." (length ready-notes))
+    ready-notes))

system/patches/patch-neuro-debug.lisp

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+(in-package :org-agent)
+
+(defun execute-openrouter-request (prompt system-prompt &key model)
+  (let ((api-key (uiop:getenv "OPENROUTER_API_KEY"))
+        (endpoint "https://openrouter.ai/api/v1/chat/completions")
+        (model-id (or model "google/gemini-2.0-flash-001")))
+    (unless api-key (return-from execute-openrouter-request "(:type :LOG :payload (:text \"OpenRouter API Key missing\"))"))
+    (kernel-log "OPENROUTER DEBUG - Using Model: ~a" model-id)
+    (let* ((headers `(("Content-Type" . "application/json")
+                      ("Authorization" . ,(format nil "Bearer ~a" api-key))
+                      ("HTTP-Referer" . "https://github.com/amr/org-agent")))
+           (body (cl-json:encode-json-to-string
+                  `((model . ,model-id)
+                    (messages . (( (role . "system") (content . ,system-prompt) )
+                                 ( (role . "user") (content . ,prompt) )))))))
+      (handler-case (let* ((response (dex:post endpoint :headers headers :content body :connect-timeout 10 :read-timeout 30)))
+                      (let ((json (cl-json:decode-json-from-string response)))
+                        (cdr (assoc :content (cdr (assoc :message (car (cdr (assoc :choices json)))))))))
+        (error (c) (format nil "(:type :LOG :payload (:text \"OpenRouter Failure: ~a\"))" c))))))

system/patches/patch-neuro-economist.lisp

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+(in-package :org-agent)
+
+(defun ask-neuro (prompt &key (system-prompt "You are the System 1 engine of a Neurosymbolic Lisp Machine.") (cascade nil) (context nil))
+  "Dispatches a neural request through the provider cascade.
+   If CASCADE is a function, it is called with CONTEXT to determine backends."
+  (let ((backends (cond
+                    ((listp cascade) cascade)
+                    ((functionp cascade) (funcall cascade context))
+                    ((functionp *provider-cascade*) (funcall *provider-cascade* context))
+                    (t *provider-cascade*))))
+    (dolist (backend backends)
+      (let ((backend-fn (gethash backend *neuro-backends*)))
+        (when backend-fn
+          (kernel-log "SYSTEM 1: Attempting backend ~a..." backend)
+          (let* (;; Consult the Economist for the model ID if the skill is available
+                 (model (ignore-errors 
+                         (uiop:symbol-call :org-agent.skills.org-skill-economist :economist-get-model-for-provider backend)))
+                 (result (if model 
+                             (funcall backend-fn prompt system-prompt :model model)
+                             (funcall backend-fn prompt system-prompt))))
+            (if (and (stringp result) (search ":LOG" result) (or (search "Failure" result) (search "missing" result)))
+                (kernel-log "SYSTEM 1: Backend ~a failed. Falling back..." backend)
+                (return-from ask-neuro result))))))
+    "(:type :LOG :payload (:text \"Neural Cascade Failure\"))"))
+
+(defun execute-openrouter-request (prompt system-prompt &key model)
+  (let ((api-key (uiop:getenv "OPENROUTER_API_KEY"))
+        (endpoint "https://openrouter.ai/api/v1/chat/completions")
+        (model-id (or model "google/gemini-2.0-flash-001")))
+    (unless api-key (return-from execute-openrouter-request "(:type :LOG :payload (:text \"OpenRouter API Key missing\"))"))
+    (let* ((headers `(("Content-Type" . "application/json")
+                      ("Authorization" . ,(format nil "Bearer ~a" api-key))
+                      ("HTTP-Referer" . "https://github.com/amr/org-agent")))
+           (body (cl-json:encode-json-to-string
+                  `((model . ,model-id)
+                    (messages . (( (role . "system") (content . ,system-prompt) )
+                                 ( (role . "user") (content . ,prompt) )))))))
+      (handler-case (let* ((response (dex:post endpoint :headers headers :content body :connect-timeout 10 :read-timeout 30))
+                           (json (cl-json:decode-json-from-string response)))
+                      (cdr (assoc :content (cdr (assoc :message (car (cdr (assoc :choices json))))))))
+        (error (c) (format nil "(:type :LOG :payload (:text \"OpenRouter Failure: ~a\"))" c))))))
+
+(defun execute-gemini-request (prompt system-prompt &key model)
+  (let* ((auth (get-provider-auth :gemini)) (api-key (getf auth :api-key)) (bearer-token (getf auth :bearer-token))
+         ;; Use model from Economist if provided, else default to pro
+         (endpoint-base (if model (format nil "https://generativelanguage.googleapis.com/v1beta/models/~a:generateContent" model)
+                            "https://generativelanguage.googleapis.com/v1beta/models/gemini-pro:generateContent")))
+    (unless (or api-key bearer-token) (return-from execute-gemini-request "(:type :LOG :payload (:text \"Authentication missing\"))"))
+    (let* ((url (if api-key (format nil "~a?key=~a" endpoint-base api-key) endpoint-base))
+           (headers `(("Content-Type" . "application/json") ,@(when bearer-token `(("Authorization" . ,(format nil "Bearer ~a" bearer-token))))))
+           (body (cl-json:encode-json-to-string `((contents . ((parts . ((text . ,(format nil "~a~%~%Prompt: ~a" system-prompt prompt))))))))))
+      (handler-case (let* ((response (dex:post url :headers headers :content body :connect-timeout 10 :read-timeout 30)) (json (cl-json:decode-json-from-string response)))
+                      (cdr (assoc :text (cdr (assoc :parts (car (cdr (assoc :parts (car (cdr (assoc :candidates json)))))))))))
+        (error (c) (format nil "(:type :LOG :payload (:text \"Neural Engine Failure: ~a\"))" c))))))

system/patches/patch-neuro-trace.lisp

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+(in-package :org-agent)
+
+(defun ask-neuro (prompt &key (system-prompt "You are the System 1 engine of a Neurosymbolic Lisp Machine.") (cascade nil) (context nil))
+  (let ((backends (cond
+                    ((listp cascade) cascade)
+                    ((functionp cascade) (funcall cascade context))
+                    ((functionp *provider-cascade*) (funcall *provider-cascade* context))
+                    (t *provider-cascade*))))
+    (dolist (backend backends)
+      (let ((backend-fn (gethash backend *neuro-backends*)))
+        (when backend-fn
+          (kernel-log "SYSTEM 1: Attempting backend ~a..." backend)
+          (let* ((model (ignore-errors 
+                         (uiop:symbol-call :org-agent.skills.org-skill-economist :economist-get-model-for-provider backend)))
+                 (result (if model 
+                             (funcall backend-fn prompt system-prompt :model model)
+                             (funcall backend-fn prompt system-prompt))))
+            (kernel-log "SYSTEM 1: Backend ~a returned: ~a" backend (if (stringp result) (subseq result 0 (min 50 (length result))) result))
+            (if (and (stringp result) (search ":LOG" result) (or (search "Failure" result) (search "missing" result)))
+                (kernel-log "SYSTEM 1: Backend ~a failed. Falling back..." backend)
+                (return-from ask-neuro result))))))
+    "(:type :LOG :payload (:text \"Neural Cascade Failure\"))"))

system/patches/patch-think-robust.lisp

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+(in-package :org-agent)
+
+(defun think (context)
+  (let ((active-skill (find-triggered-skill context)))
+    (if active-skill
+        (progn
+          (kernel-log "SYSTEM 1: Engaging skill '~a'~%" (skill-name active-skill))
+          (let* ((prompt-generator (skill-neuro-prompt active-skill)) 
+                 (prompt (when prompt-generator (funcall prompt-generator context))))
+            (if prompt 
+                (let* ((thought (ask-neuro prompt :context context))
+                       ;; Improved cleaning: Extract content between ``` blocks if they exist
+                       (cleaned-thought 
+                        (let ((match (cl-ppcre:scan-to-strings "(?s)```(?:lisp)?\\n?(.*?)\\n?```" thought)))
+                          (if match
+                              (let ((regs (nth-value 1 (cl-ppcre:scan-to-strings "(?s)```(?:lisp)?\\n?(.*?)\\n?```" thought))))
+                                (if (and regs (> (length regs) 0)) (elt regs 0) thought))
+                              (string-trim '(#\Space #\Newline #\Tab) thought))))
+                       (suggestion (ignore-errors (read-from-string cleaned-thought))))
+                  (kernel-log "SYSTEM 1 Suggestion: ~a~%" cleaned-thought)
+                  (cond
+                    ((and suggestion (listp suggestion)) suggestion)
+                    ;; SALVAGE: If LLM returned plain text or a non-list symbol
+                    ((and (let ((p (getf context :payload))) (eq (getf p :sensor) :chat-message))
+                          (> (length cleaned-thought) 0))
+                     (kernel-log "SYSTEM 1: SALVAGING plain-text response.~%")
+                     (let* ((no-prefix (cl-ppcre:regex-replace "(?i)^(okay,? |sure,? |i will |i've |i have |here is |got it\\.? |understood\\.? |done\\.? |yes,? )+" cleaned-thought "")))
+                       `(:target :emacs :payload (:action :insert-at-end :buffer "*org-agent-chat*" :text ,no-prefix))))
+                    (t 
+                     (kernel-log "SYSTEM 1 ERROR: Could not parse response as Lisp plist.~%")
+                     nil)))
+                nil)))
+        nil)))

system/plans/flight-plan-structural-cleanup.org

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+* Flight Plan: Structural Cleanup and Patch Management
+:PROPERTIES:
+:STATUS: IN-PROGRESS
+:END:
+
+** Analyst Phase
+The workspace currently contains structural irregularities that violate the PARA and Zero-Bloat invariants:
+1. Broken project directories: =projectsorg-skill-web-research= and =projectsorg-skill-workspace-manager= exist in the root due to a previous path concatenation error.
+2. Root clutter: Seven =patch-*.lisp= files are located in the root directory, making system maintenance difficult.
+3. Git Status: Recent changes have been pushed, but these structural fixes need to be atomically committed.
+
+** Coder Phase
+- [X] Create =system/patches/= directory if not already present.
+- [X] Move =projectsorg-skill-web-research= to =projects/org-skill-web-research=.
+- [X] Move =projectsorg-skill-workspace-manager= to =projects/org-skill-workspace-manager=.
+- [X] Move all =patch-*.lisp= files to =system/patches/=.
+- [ ] Stage deletions and new paths in git.
+- [ ] Commit with message: "chore: structural cleanup of projects and patches"
+- [ ] Push to origin main.
+
+** Tester Phase
+- [ ] Verify that =projects/org-skill-web-research/tests/test-suite.lisp= exists and is accessible.
+- [ ] Verify that =projects/org-skill-workspace-manager/tests/test-suite.lisp= exists and is accessible.
+- [ ] List =system/patches/= to confirm all seven patches are accounted for.
+- [ ] Verify =git status= is clean.