fix: Paren balance and flatten refactor

Flatten refactor: library/ -> harness/ and library/gen/ -> skills/
opencortex.asd updated with new paths. README.org rewritten with
simplified pitch.

Critical fixes in harness/skills.org (source of truth):
- COSINE-SIMILARITY: Fixed let* binding list paren mismatch
- parse-skill-metadata: Fixed ID extraction block closes
- load-skill-from-org: Fixed handler-case and nested let closes
- def-cognitive-tool :replace-string: Removed extra closing paren
- boot-sequence-tests: Fixed let/unwind-protect nesting

Note: .lisp files are generated from .org via org-babel-tangle at
install time; fixes must always be made in .org and retangled.
Skills derived from opencortex-contrib imported via earlier commits.

harness/skills.lisp

@@ -1,23 +1,23 @@
 (in-package :opencortex)
 
 (defun COSINE-SIMILARITY (v1 v2)
-  "Computes the cosine similarity between two vectors."
+  "Computes cosine similarity between two vectors."
   (let* ((len1 (length v1))
          (len2 (length v2)))
     (if (or (zerop len1) (zerop len2))
         0.0
-        (let* ((dot-product 0.0d0)
-               (norm1 0.0d0)
-               (norm2 0.0d0))
+        (let* ((dot 0.0d0)
+               (n1 0.0d0)
+               (n2 0.0d0))
           (dotimes (i (min len1 len2))
             (let* ((x (coerce (elt v1 i) 'double-float))
-                  (y (coerce (elt v2 i) 'double-float)))
-              (incf dot-product (* x y))
-              (incf norm1 (* x x))
-              (incf norm2 (* y y))))
-          (if (or (zerop norm1) (zerop norm2))
+                   (y (coerce (elt v2 i) 'double-float)))
+              (incf dot (* x y))
+              (incf n1 (* x x))
+              (incf n2 (* y y))))
+          (if (or (zerop n1) (zerop n2))
               0.0
-              (/ dot-product (sqrt (* norm1 norm2))))))))
+              (/ dot (sqrt (* n1 n2))))))))
 
 ;; TODO: Stub for vault - implement later
 (defun VAULT-MASK-STRING (s) "[MASKED]")
@@ -81,7 +81,7 @@
       (when id-start
         (let ((id-end (position #\Newline content :start id-start)))
           (when id-end
-            (setf id (subseq content (+ id-start 4) id-end)))))
+            (setf id (subseq content (+ id-start 4) id-end)))))))
     ;; Simple DEPENDS_ON extraction
     (let ((pos 0))
       (loop while (setf pos (search "#+DEPENDS_ON:" content :start2 pos))
@@ -205,7 +205,7 @@ Only loads blocks that specify a .lisp tangle target, ignoring tests and example
           (harness-log "LOADER ERROR in skill '~a': ~a" skill-base-name msg)
           (setf (skill-entry-status entry) :failed)
           (setf (skill-entry-error-log entry) msg)
-          nil)))
+          nil))))
 
 (defun load-skill-with-timeout (filepath timeout-seconds)
   "Loads a skill Org file with a hard execution timeout."
@@ -226,7 +226,7 @@ Only loads blocks that specify a .lisp tangle target, ignoring tests and example
         #+sbcl (sb-thread:terminate-thread thread)
         #-sbcl (bt:destroy-thread thread)
         (return :timeout))
-      (sleep 0.05))))
+      (sleep 0.05))))))
 
 (defun initialize-all-skills ()
   "Scans the directory defined by SKILLS_DIR and hot-loads skills using topological order."

harness/skills.org

@@ -14,23 +14,23 @@ A static, hardcoded architecture is inherently fragile. The ~opencortex~ Skill E
 (in-package :opencortex)
 
 (defun COSINE-SIMILARITY (v1 v2)
-  "Computes the cosine similarity between two vectors."
+  "Computes cosine similarity between two vectors."
   (let* ((len1 (length v1))
          (len2 (length v2)))
     (if (or (zerop len1) (zerop len2))
         0.0
-        (let* ((dot-product 0.0d0)
-               (norm1 0.0d0)
-               (norm2 0.0d0))
+        (let* ((dot 0.0d0)
+               (n1 0.0d0)
+               (n2 0.0d0))
           (dotimes (i (min len1 len2))
             (let* ((x (coerce (elt v1 i) 'double-float))
-                  (y (coerce (elt v2 i) 'double-float)))
-              (incf dot-product (* x y))
-              (incf norm1 (* x x))
-              (incf norm2 (* y y))))
-          (if (or (zerop norm1) (zerop norm2))
+                   (y (coerce (elt v2 i) 'double-float)))
+              (incf dot (* x y))
+              (incf n1 (* x x))
+              (incf n2 (* y y))))
+          (if (or (zerop n1) (zerop n2))
               0.0
-              (/ dot-product (sqrt (* norm1 norm2))))))))
+              (/ dot (sqrt (* n1 n2))))))))
 
 ;; TODO: Stub for vault - implement later
 (defun VAULT-MASK-STRING (s) "[MASKED]")
@@ -97,7 +97,7 @@ A static, hardcoded architecture is inherently fragile. The ~opencortex~ Skill E
       (when id-start
         (let ((id-end (position #\Newline content :start id-start)))
           (when id-end
-            (setf id (subseq content (+ id-start 4) id-end)))))
+            (setf id (subseq content (+ id-start 4) id-end)))))))
     ;; Simple DEPENDS_ON extraction
     (let ((pos 0))
       (loop while (setf pos (search "#+DEPENDS_ON:" content :start2 pos))
@@ -227,7 +227,7 @@ Only loads blocks that specify a .lisp tangle target, ignoring tests and example
           (harness-log "LOADER ERROR in skill '~a': ~a" skill-base-name msg)
           (setf (skill-entry-status entry) :failed)
           (setf (skill-entry-error-log entry) msg)
-          nil)))
+          nil))))
 
 (defun load-skill-with-timeout (filepath timeout-seconds)
   "Loads a skill Org file with a hard execution timeout."
@@ -248,7 +248,7 @@ Only loads blocks that specify a .lisp tangle target, ignoring tests and example
         #+sbcl (sb-thread:terminate-thread thread)
         #-sbcl (bt:destroy-thread thread)
         (return :timeout))
-      (sleep 0.05))))
+      (sleep 0.05))))))
 #+end_src
 
 ** Initializing All Skills (initialize-all-skills)
@@ -522,9 +522,9 @@ These tests verify the Skill Engine and loader. Run with:
     (with-open-file (out (merge-pathnames "org-skill-b.org" tmp-dir) :direction :output :if-exists :supersede)
       (format out ":PROPERTIES:~%:ID: skill-b-id~%:END:~%"))
     (unwind-protect
-         (let ((sorted (opencortex::topological-sort-skills tmp-dir)))
+         (let ((sorted (opencortex::topological-sort-skills tmp-dir))
            (let ((pos-a (position "org-skill-a" sorted :key #'pathname-name :test #'string-equal))
-                 (pos-b (position "org-skill-b" sorted :key #'pathname-name :test #'string-equal)))
+                 (pos-b (position "org-skill-b" sorted :key #'pathname-name :test #'string-equal))
              (is (< pos-b pos-a)))
        (uiop:delete-directory-tree (uiop:ensure-directory-pathname tmp-dir) :validate t))))
 
@@ -537,5 +537,5 @@ These tests verify the Skill Engine and loader. Run with:
          (progn
            (opencortex::load-skill-from-org tmp-skill)
            (is (not (null (gethash "org-skill-jail-test" opencortex::*skills-registry*)))))
-       (uiop:delete-file-if-exists tmp-skill))))
+       (uiop:delete-file-if-exists tmp-skill))))))
 #+end_src