From 8c318471acf55e403b4d7629f833098b8b86be96 Mon Sep 17 00:00:00 2001
From: ysun67 <ysun67@syr.edu>
Date: Fri, 17 Jul 2026 15:49:34 -0400
Subject: [PATCH 1/2] Remove stale worktree gitlinks

---
 .claude/worktrees/agent-a0887fdee3510e86f | 1 -
 .claude/worktrees/agent-a0c836f04d21a7413 | 1 -
 .claude/worktrees/agent-a13563de836f67ac7 | 1 -
 .claude/worktrees/agent-a171f14d181124637 | 1 -
 .claude/worktrees/agent-a1a104366d617f22e | 1 -
 .claude/worktrees/agent-a1ab1cd2bbdd22d8d | 1 -
 .claude/worktrees/agent-a1c6b6d99c198e457 | 1 -
 .claude/worktrees/agent-a1d137564c62a6290 | 1 -
 .claude/worktrees/agent-a1d912191c716d37b | 1 -
 .claude/worktrees/agent-a24d347aeb8a1bae2 | 1 -
 .claude/worktrees/agent-a24d950c2b50b0ce0 | 1 -
 .claude/worktrees/agent-a26a54ab4027866f1 | 1 -
 .claude/worktrees/agent-a29c10e3a0bfc9f00 | 1 -
 .claude/worktrees/agent-a35bf8b3181762040 | 1 -
 .claude/worktrees/agent-a36ec61a3d0f2a3d3 | 1 -
 .claude/worktrees/agent-a3ac224bdbc08be50 | 1 -
 .claude/worktrees/agent-a3da655562484cfef | 1 -
 .claude/worktrees/agent-a3f1f8ebfd28fc03d | 1 -
 .claude/worktrees/agent-a42db4bf883cc0d1b | 1 -
 .claude/worktrees/agent-a480a1e0e9be42c82 | 1 -
 .claude/worktrees/agent-a49197e82edb42cc8 | 1 -
 .claude/worktrees/agent-a4de8737554ba6aa4 | 1 -
 .claude/worktrees/agent-a56c9650ee5a94158 | 1 -
 .claude/worktrees/agent-a6570c6d0a9f33cd3 | 1 -
 .claude/worktrees/agent-a6b667a17f179b0ad | 1 -
 .claude/worktrees/agent-a7287304fc234d7fe | 1 -
 .claude/worktrees/agent-a73b9012cf98ff7a7 | 1 -
 .claude/worktrees/agent-a79a02ee3033ccea4 | 1 -
 .claude/worktrees/agent-a7ddbc390758a3802 | 1 -
 .claude/worktrees/agent-a825517f95ce847ea | 1 -
 .claude/worktrees/agent-a88d447fa7a5a380c | 1 -
 .claude/worktrees/agent-a8f6a2a930f9cd270 | 1 -
 .claude/worktrees/agent-a95f48090051e7c41 | 1 -
 .claude/worktrees/agent-a9e8303f5bcaeced2 | 1 -
 .claude/worktrees/agent-a9ed629133905a183 | 1 -
 .claude/worktrees/agent-aa5e808d0ff68a7fd | 1 -
 .claude/worktrees/agent-ab05f854a47c99775 | 1 -
 .claude/worktrees/agent-abd1bd6eb13210b6c | 1 -
 .claude/worktrees/agent-abd6106a232fd1b99 | 1 -
 .claude/worktrees/agent-ac076bf38fdf880cf | 1 -
 .claude/worktrees/agent-ac68ee48a9d01178c | 1 -
 .claude/worktrees/agent-ac6b5738daabefe37 | 1 -
 .claude/worktrees/agent-acb48c7899359e1ae | 1 -
 .claude/worktrees/agent-ad34932b729e9987b | 1 -
 .claude/worktrees/agent-ad4270784f2327383 | 1 -
 .claude/worktrees/agent-ada998c6ce03e24ea | 1 -
 .claude/worktrees/agent-adb368fecfff1a049 | 1 -
 .claude/worktrees/agent-af33119eed489338e | 1 -
 .claude/worktrees/agent-af4fef22c344d4da6 | 1 -
 .claude/worktrees/agent-af540d582550cd7ef | 1 -
 .claude/worktrees/agent-afe05d0ca6f1080af | 1 -
 .claude/worktrees/pr-1c-target-kwarg      | 1 -
 52 files changed, 52 deletions(-)
 delete mode 160000 .claude/worktrees/agent-a0887fdee3510e86f
 delete mode 160000 .claude/worktrees/agent-a0c836f04d21a7413
 delete mode 160000 .claude/worktrees/agent-a13563de836f67ac7
 delete mode 160000 .claude/worktrees/agent-a171f14d181124637
 delete mode 160000 .claude/worktrees/agent-a1a104366d617f22e
 delete mode 160000 .claude/worktrees/agent-a1ab1cd2bbdd22d8d
 delete mode 160000 .claude/worktrees/agent-a1c6b6d99c198e457
 delete mode 160000 .claude/worktrees/agent-a1d137564c62a6290
 delete mode 160000 .claude/worktrees/agent-a1d912191c716d37b
 delete mode 160000 .claude/worktrees/agent-a24d347aeb8a1bae2
 delete mode 160000 .claude/worktrees/agent-a24d950c2b50b0ce0
 delete mode 160000 .claude/worktrees/agent-a26a54ab4027866f1
 delete mode 160000 .claude/worktrees/agent-a29c10e3a0bfc9f00
 delete mode 160000 .claude/worktrees/agent-a35bf8b3181762040
 delete mode 160000 .claude/worktrees/agent-a36ec61a3d0f2a3d3
 delete mode 160000 .claude/worktrees/agent-a3ac224bdbc08be50
 delete mode 160000 .claude/worktrees/agent-a3da655562484cfef
 delete mode 160000 .claude/worktrees/agent-a3f1f8ebfd28fc03d
 delete mode 160000 .claude/worktrees/agent-a42db4bf883cc0d1b
 delete mode 160000 .claude/worktrees/agent-a480a1e0e9be42c82
 delete mode 160000 .claude/worktrees/agent-a49197e82edb42cc8
 delete mode 160000 .claude/worktrees/agent-a4de8737554ba6aa4
 delete mode 160000 .claude/worktrees/agent-a56c9650ee5a94158
 delete mode 160000 .claude/worktrees/agent-a6570c6d0a9f33cd3
 delete mode 160000 .claude/worktrees/agent-a6b667a17f179b0ad
 delete mode 160000 .claude/worktrees/agent-a7287304fc234d7fe
 delete mode 160000 .claude/worktrees/agent-a73b9012cf98ff7a7
 delete mode 160000 .claude/worktrees/agent-a79a02ee3033ccea4
 delete mode 160000 .claude/worktrees/agent-a7ddbc390758a3802
 delete mode 160000 .claude/worktrees/agent-a825517f95ce847ea
 delete mode 160000 .claude/worktrees/agent-a88d447fa7a5a380c
 delete mode 160000 .claude/worktrees/agent-a8f6a2a930f9cd270
 delete mode 160000 .claude/worktrees/agent-a95f48090051e7c41
 delete mode 160000 .claude/worktrees/agent-a9e8303f5bcaeced2
 delete mode 160000 .claude/worktrees/agent-a9ed629133905a183
 delete mode 160000 .claude/worktrees/agent-aa5e808d0ff68a7fd
 delete mode 160000 .claude/worktrees/agent-ab05f854a47c99775
 delete mode 160000 .claude/worktrees/agent-abd1bd6eb13210b6c
 delete mode 160000 .claude/worktrees/agent-abd6106a232fd1b99
 delete mode 160000 .claude/worktrees/agent-ac076bf38fdf880cf
 delete mode 160000 .claude/worktrees/agent-ac68ee48a9d01178c
 delete mode 160000 .claude/worktrees/agent-ac6b5738daabefe37
 delete mode 160000 .claude/worktrees/agent-acb48c7899359e1ae
 delete mode 160000 .claude/worktrees/agent-ad34932b729e9987b
 delete mode 160000 .claude/worktrees/agent-ad4270784f2327383
 delete mode 160000 .claude/worktrees/agent-ada998c6ce03e24ea
 delete mode 160000 .claude/worktrees/agent-adb368fecfff1a049
 delete mode 160000 .claude/worktrees/agent-af33119eed489338e
 delete mode 160000 .claude/worktrees/agent-af4fef22c344d4da6
 delete mode 160000 .claude/worktrees/agent-af540d582550cd7ef
 delete mode 160000 .claude/worktrees/agent-afe05d0ca6f1080af
 delete mode 160000 .claude/worktrees/pr-1c-target-kwarg

diff --git a/.claude/worktrees/agent-a0887fdee3510e86f b/.claude/worktrees/agent-a0887fdee3510e86f
deleted file mode 160000
index 882ed10..0000000
--- a/.claude/worktrees/agent-a0887fdee3510e86f
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 882ed1078d34df13999fdcad05cc254c3ddac6eb
diff --git a/.claude/worktrees/agent-a0c836f04d21a7413 b/.claude/worktrees/agent-a0c836f04d21a7413
deleted file mode 160000
index 0e8f751..0000000
--- a/.claude/worktrees/agent-a0c836f04d21a7413
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 0e8f7519544fd44f66ff8a03a5a3baafc5fc7d5c
diff --git a/.claude/worktrees/agent-a13563de836f67ac7 b/.claude/worktrees/agent-a13563de836f67ac7
deleted file mode 160000
index f9df620..0000000
--- a/.claude/worktrees/agent-a13563de836f67ac7
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f9df62006756acea434b14111543c7db92bf53cb
diff --git a/.claude/worktrees/agent-a171f14d181124637 b/.claude/worktrees/agent-a171f14d181124637
deleted file mode 160000
index 3922846..0000000
--- a/.claude/worktrees/agent-a171f14d181124637
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 39228463b5d44e6dc51ecdb581a3d7920564aae3
diff --git a/.claude/worktrees/agent-a1a104366d617f22e b/.claude/worktrees/agent-a1a104366d617f22e
deleted file mode 160000
index b83cf76..0000000
--- a/.claude/worktrees/agent-a1a104366d617f22e
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit b83cf760f99ade36207fda4f0498745f230e5da1
diff --git a/.claude/worktrees/agent-a1ab1cd2bbdd22d8d b/.claude/worktrees/agent-a1ab1cd2bbdd22d8d
deleted file mode 160000
index 27eb27c..0000000
--- a/.claude/worktrees/agent-a1ab1cd2bbdd22d8d
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 27eb27caa2b58462cce5030cda6502ff3ec6acc2
diff --git a/.claude/worktrees/agent-a1c6b6d99c198e457 b/.claude/worktrees/agent-a1c6b6d99c198e457
deleted file mode 160000
index e804035..0000000
--- a/.claude/worktrees/agent-a1c6b6d99c198e457
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e804035e6254b0eb93f54c94424ef7886fe4fd70
diff --git a/.claude/worktrees/agent-a1d137564c62a6290 b/.claude/worktrees/agent-a1d137564c62a6290
deleted file mode 160000
index f522d21..0000000
--- a/.claude/worktrees/agent-a1d137564c62a6290
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f522d21b61439d24734f731551770355732ca371
diff --git a/.claude/worktrees/agent-a1d912191c716d37b b/.claude/worktrees/agent-a1d912191c716d37b
deleted file mode 160000
index c310407..0000000
--- a/.claude/worktrees/agent-a1d912191c716d37b
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit c31040729342feb5414e9d9d29e959835af1c52c
diff --git a/.claude/worktrees/agent-a24d347aeb8a1bae2 b/.claude/worktrees/agent-a24d347aeb8a1bae2
deleted file mode 160000
index c46b87c..0000000
--- a/.claude/worktrees/agent-a24d347aeb8a1bae2
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit c46b87ce309292c448e617a43ea19472557ff780
diff --git a/.claude/worktrees/agent-a24d950c2b50b0ce0 b/.claude/worktrees/agent-a24d950c2b50b0ce0
deleted file mode 160000
index 605dbca..0000000
--- a/.claude/worktrees/agent-a24d950c2b50b0ce0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 605dbca01b1f072a557861b6c77ca9170c3c44e2
diff --git a/.claude/worktrees/agent-a26a54ab4027866f1 b/.claude/worktrees/agent-a26a54ab4027866f1
deleted file mode 160000
index 5be94d3..0000000
--- a/.claude/worktrees/agent-a26a54ab4027866f1
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 5be94d35c376a667b465550ceccb4569815d556c
diff --git a/.claude/worktrees/agent-a29c10e3a0bfc9f00 b/.claude/worktrees/agent-a29c10e3a0bfc9f00
deleted file mode 160000
index 34e224a..0000000
--- a/.claude/worktrees/agent-a29c10e3a0bfc9f00
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 34e224a6c80755557ce58feafaf138d18cd3ec69
diff --git a/.claude/worktrees/agent-a35bf8b3181762040 b/.claude/worktrees/agent-a35bf8b3181762040
deleted file mode 160000
index 2c6b32f..0000000
--- a/.claude/worktrees/agent-a35bf8b3181762040
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 2c6b32fdb65a1d73929cda469ab84299419da97f
diff --git a/.claude/worktrees/agent-a36ec61a3d0f2a3d3 b/.claude/worktrees/agent-a36ec61a3d0f2a3d3
deleted file mode 160000
index 8f41884..0000000
--- a/.claude/worktrees/agent-a36ec61a3d0f2a3d3
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 8f41884a7053f6172f72a5d52fe985fc3ed57bf4
diff --git a/.claude/worktrees/agent-a3ac224bdbc08be50 b/.claude/worktrees/agent-a3ac224bdbc08be50
deleted file mode 160000
index 0ce01a0..0000000
--- a/.claude/worktrees/agent-a3ac224bdbc08be50
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 0ce01a0dd188a3033f01182ea27f451dcacf9599
diff --git a/.claude/worktrees/agent-a3da655562484cfef b/.claude/worktrees/agent-a3da655562484cfef
deleted file mode 160000
index 3829a14..0000000
--- a/.claude/worktrees/agent-a3da655562484cfef
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 3829a14ebe9eecea01638b7795d3b85c25de252c
diff --git a/.claude/worktrees/agent-a3f1f8ebfd28fc03d b/.claude/worktrees/agent-a3f1f8ebfd28fc03d
deleted file mode 160000
index 5f8ad88..0000000
--- a/.claude/worktrees/agent-a3f1f8ebfd28fc03d
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 5f8ad8881091629ceef5e7c36c22e43d11aca51e
diff --git a/.claude/worktrees/agent-a42db4bf883cc0d1b b/.claude/worktrees/agent-a42db4bf883cc0d1b
deleted file mode 160000
index b33d05c..0000000
--- a/.claude/worktrees/agent-a42db4bf883cc0d1b
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit b33d05c72897d00ac9e5d6229e0d81980d4d00ad
diff --git a/.claude/worktrees/agent-a480a1e0e9be42c82 b/.claude/worktrees/agent-a480a1e0e9be42c82
deleted file mode 160000
index c217d34..0000000
--- a/.claude/worktrees/agent-a480a1e0e9be42c82
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit c217d341d2edc17a1ebf07ccceaabdb49636d06c
diff --git a/.claude/worktrees/agent-a49197e82edb42cc8 b/.claude/worktrees/agent-a49197e82edb42cc8
deleted file mode 160000
index adfe381..0000000
--- a/.claude/worktrees/agent-a49197e82edb42cc8
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit adfe381e18fc828339d9d5b87c8b04b4e55a1fd9
diff --git a/.claude/worktrees/agent-a4de8737554ba6aa4 b/.claude/worktrees/agent-a4de8737554ba6aa4
deleted file mode 160000
index 5b2810c..0000000
--- a/.claude/worktrees/agent-a4de8737554ba6aa4
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 5b2810ca1bef78c846eaa121deef8c407c53d8b6
diff --git a/.claude/worktrees/agent-a56c9650ee5a94158 b/.claude/worktrees/agent-a56c9650ee5a94158
deleted file mode 160000
index 5b28bdb..0000000
--- a/.claude/worktrees/agent-a56c9650ee5a94158
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 5b28bdb5cea88d7f3f95730274ce0639f60211cb
diff --git a/.claude/worktrees/agent-a6570c6d0a9f33cd3 b/.claude/worktrees/agent-a6570c6d0a9f33cd3
deleted file mode 160000
index f737eb1..0000000
--- a/.claude/worktrees/agent-a6570c6d0a9f33cd3
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f737eb115b06589516f3c530e6b15c221159b23f
diff --git a/.claude/worktrees/agent-a6b667a17f179b0ad b/.claude/worktrees/agent-a6b667a17f179b0ad
deleted file mode 160000
index 7e3892c..0000000
--- a/.claude/worktrees/agent-a6b667a17f179b0ad
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 7e3892cb8ec5d75d9efaa206bf8d17a6be590641
diff --git a/.claude/worktrees/agent-a7287304fc234d7fe b/.claude/worktrees/agent-a7287304fc234d7fe
deleted file mode 160000
index ef5003d..0000000
--- a/.claude/worktrees/agent-a7287304fc234d7fe
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ef5003d82a6d5a306d434ddf892b27f2d4c77e5a
diff --git a/.claude/worktrees/agent-a73b9012cf98ff7a7 b/.claude/worktrees/agent-a73b9012cf98ff7a7
deleted file mode 160000
index fa01de8..0000000
--- a/.claude/worktrees/agent-a73b9012cf98ff7a7
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit fa01de886b2392a37f671ee2655262f0f3d0a6df
diff --git a/.claude/worktrees/agent-a79a02ee3033ccea4 b/.claude/worktrees/agent-a79a02ee3033ccea4
deleted file mode 160000
index c85cde8..0000000
--- a/.claude/worktrees/agent-a79a02ee3033ccea4
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit c85cde8af33a9efc057b41eb8f864c0252dcbb3c
diff --git a/.claude/worktrees/agent-a7ddbc390758a3802 b/.claude/worktrees/agent-a7ddbc390758a3802
deleted file mode 160000
index 3e726f0..0000000
--- a/.claude/worktrees/agent-a7ddbc390758a3802
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 3e726f0dd5931c2f2944fdc474fc6c36503d95f1
diff --git a/.claude/worktrees/agent-a825517f95ce847ea b/.claude/worktrees/agent-a825517f95ce847ea
deleted file mode 160000
index 7cf5212..0000000
--- a/.claude/worktrees/agent-a825517f95ce847ea
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 7cf52126a37842ab4ae814196911559520be044f
diff --git a/.claude/worktrees/agent-a88d447fa7a5a380c b/.claude/worktrees/agent-a88d447fa7a5a380c
deleted file mode 160000
index e4497e4..0000000
--- a/.claude/worktrees/agent-a88d447fa7a5a380c
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e4497e46046c094fa1a08674ba887b17d0db3c19
diff --git a/.claude/worktrees/agent-a8f6a2a930f9cd270 b/.claude/worktrees/agent-a8f6a2a930f9cd270
deleted file mode 160000
index a3f1680..0000000
--- a/.claude/worktrees/agent-a8f6a2a930f9cd270
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit a3f16806159faf037f1c759c91a30c424c40547b
diff --git a/.claude/worktrees/agent-a95f48090051e7c41 b/.claude/worktrees/agent-a95f48090051e7c41
deleted file mode 160000
index 86c64f2..0000000
--- a/.claude/worktrees/agent-a95f48090051e7c41
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 86c64f2db7758d641f234d1d3215b5ff02b0d8b1
diff --git a/.claude/worktrees/agent-a9e8303f5bcaeced2 b/.claude/worktrees/agent-a9e8303f5bcaeced2
deleted file mode 160000
index 85bd4f6..0000000
--- a/.claude/worktrees/agent-a9e8303f5bcaeced2
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 85bd4f657f95fd29d8e432295bf4b4d2da58dfb8
diff --git a/.claude/worktrees/agent-a9ed629133905a183 b/.claude/worktrees/agent-a9ed629133905a183
deleted file mode 160000
index 3f268f5..0000000
--- a/.claude/worktrees/agent-a9ed629133905a183
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 3f268f5bc6e2fbd51c6fa42b6a9e4868a8a87cc8
diff --git a/.claude/worktrees/agent-aa5e808d0ff68a7fd b/.claude/worktrees/agent-aa5e808d0ff68a7fd
deleted file mode 160000
index 981b0e4..0000000
--- a/.claude/worktrees/agent-aa5e808d0ff68a7fd
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 981b0e440b6c32c19f57b3b6bf391b57b7515a0f
diff --git a/.claude/worktrees/agent-ab05f854a47c99775 b/.claude/worktrees/agent-ab05f854a47c99775
deleted file mode 160000
index a671976..0000000
--- a/.claude/worktrees/agent-ab05f854a47c99775
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit a671976d24f491af5ccb7b5d1ab986678cff020f
diff --git a/.claude/worktrees/agent-abd1bd6eb13210b6c b/.claude/worktrees/agent-abd1bd6eb13210b6c
deleted file mode 160000
index e85f616..0000000
--- a/.claude/worktrees/agent-abd1bd6eb13210b6c
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e85f6163c141dfd342c220fb128dcfe55eb2661e
diff --git a/.claude/worktrees/agent-abd6106a232fd1b99 b/.claude/worktrees/agent-abd6106a232fd1b99
deleted file mode 160000
index 7c3a726..0000000
--- a/.claude/worktrees/agent-abd6106a232fd1b99
+++ /dev/null
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From f82e54ef72436fdbc1df78cf42269cfb9c5d0bdc Mon Sep 17 00:00:00 2001
From: Colton Payne <coltonpayne23@gmail.com>
Date: Fri, 21 Aug 2026 11:19:54 -0400
Subject: [PATCH 2/2] Add VulReasoner phase-2 runner + trace-parity contract

TRACE_PARITY_CONTRACT.md is the phase-2 equivalence spec (previously
uncommitted, existed only on Colton's laptop and leibniz). run_vr_phase2.py
runs one real trajectory's analyst fragment on SRDatalog per that contract:
generalized ingest (per-trajectory hasLabel bounds, stepFrom windows, --kg /
--end-time), native transitive closure for the kg_property analyst
connectors, and per-rule witness relations emitting full qualified grounding
sets (contract Tier 1). Conformance results live in vulreasoner-mindset
branch hybrid-parity-harness (hybrid_e2e_check.py): Tier-1/Tier-2 and
end-to-end composed-trace equality PASS on both pinned trajectories.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 minimal_vulreasoner/TRACE_PARITY_CONTRACT.md | 245 ++++++++++++
 minimal_vulreasoner/run_vr_phase2.py         | 389 +++++++++++++++++++
 2 files changed, 634 insertions(+)
 create mode 100644 minimal_vulreasoner/TRACE_PARITY_CONTRACT.md
 create mode 100644 minimal_vulreasoner/run_vr_phase2.py

diff --git a/minimal_vulreasoner/TRACE_PARITY_CONTRACT.md b/minimal_vulreasoner/TRACE_PARITY_CONTRACT.md
new file mode 100644
index 0000000..cb7e7c1
--- /dev/null
+++ b/minimal_vulreasoner/TRACE_PARITY_CONTRACT.md
@@ -0,0 +1,245 @@
+# Trace-parity contract (v1)
+
+**Scope:** the minimal VulReasoner subset. **Parties:** the PyReason oracle
+(as consumed by VulReasoner's `trace_conversion.py` / `filter_reasoning_trace.py`)
+and any SRDatalog implementation claiming trace parity (e.g. the
+`srdatalog.pyreason` frontend of PR #2).
+
+This document defines *what "the SRDatalog trace matches PyReason" means* —
+precisely enough to implement against and to test mechanically. It deliberately
+does **not** require reproducing PyReason's `get_rule_trace` operation
+chronology; §5 proves that within scope no chronology is needed.
+
+Field names below refer to VulReasoner's `ReasoningStep`
+(`vulreasoner-mindset/src/trace_conversion.py`), the struct every downstream
+consumer reads. Empirical claims about PyReason's CSV output were verified
+against real traces in `vulreasoner-mindset/outputs/traces_api/CWE_121_MVP2/`.
+
+---
+
+## 1. Scoped program fragment
+
+The contract covers exactly the programs expressible in
+`minimal_vulreasoner/`:
+
+| Element | Allowed forms |
+|---|---|
+| Rules | the six analyst rules of `rules/analyst_rules.csv`: head `analystAt(CB2):paired_minimum_bounds_ann_fn`, delay `<-1`, body = `analystAt(CB1):[0.25,1]`, `hasLabel(CB1,·):[0.1,1]`, `hasLabel(CB2,·):[0.1,1]`, `connector(·,·):[0.1,1]`, `stepFrom(CB1,CB2)` |
+| Annotation fn | `paired_minimum_bounds_ann_fn` only |
+| Closed world | `analystAt` (fixed finite domain) |
+| Facts | static `hasLabel(entity,label)`; timed `analystAt(seed)` on `[0,1]`; timed `stepFrom(bᵢ,bᵢ₊₁)` on `[i+1,i+2]`; KG attributes via `load_graphml` + `save_graph_attributes_to_trace` |
+| Settings | `atom_trace=True`, `allow_ground_rules=True`, `save_graph_attributes_to_trace=True`, `persistent=False` (default) |
+| Run | `pr.reason(timesteps=END_TIME)` |
+
+**Excluded** (out of contract, not merely untested): `<-0` rules (label
+rules), the `closed_rule.csv` pair (`future`, negated-head
+`inconsistent_rule`), `set_static` heads, binary heads with `infer_edges`
+domain growth, the `obs` layer and ground-atom registration, `persistent=True`,
+multi-KG orchestration, and `generalized_minimum_bounds_ann_fn`. Every one of
+these invalidates at least one lemma in §5; extending the contract to them
+requires a new version, not a relaxation.
+
+## 2. The canonical trace record
+
+Both engines must be renderable into a common form. One **record** corresponds
+to one row of PyReason's rule-trace CSVs (one `ReasoningStep`):
+
+```
+Record = (
+  time            : int,                     # logical timestep
+  label           : str,                     # predicate name
+  term            : Node(id) | Edge(a, b),   # 1-ary → Node, 2-ary → Edge
+  due_to          : str,                     # rule name or fact name
+  triggered_by    : "Fact" | "Rule",
+  consistent      : bool,
+  clause_sets     : tuple[frozenset[Term], ...],  # per body-clause position; () for facts
+  inconsistency_message : None,              # always None in scope
+)
+```
+
+plus, per record, `old_bound` and `new_bound` (handled separately in §4 —
+they are *not* part of the canonical identity because intermediate bounds are
+order-sensitive when several updates hit one key).
+
+Canonicalization rules:
+
+- **term**: PyReason writes 1-ary atoms to the node CSV (`term = {"node": id}`)
+  and 2-ary atoms to the edge CSV (`term = {"edge": (a, b)}`). The SRDatalog
+  side must classify identically by predicate arity.
+- **clause_sets**: parse each `Clause-i` cell with `ast.literal_eval`; map each
+  grounding through `grounding_to_term` semantics (bare string or 1-tuple →
+  Node, n-tuple → Edge); collect **as a set**, position-aligned with the
+  rule's body clauses in source order. Ordering *inside* a clause cell is
+  PyReason predicate-map admission order and is explicitly **not** part of the
+  contract. Facts have `clause_sets = ()`.
+- **key** of a record group: `(label, term, time)` — this matches
+  `filter_reasoning_trace.index_steps` (note: that index ignores `time`; the
+  contract still groups by time because §3's multiset equality subsumes the
+  coarser index).
+
+## 3. Tier 1 — firing-multiset equality (REQUIRED)
+
+> The **multiset** of canonical records produced by the two engines over the
+> full run must be equal.
+
+This is the load-bearing requirement. It implies, without further clauses:
+
+- `num_inferences` parity (it is `len(combined_trace)`),
+- `input_valid` parity (§6; all records must have `consistent = True`),
+- `base_filter` output parity — the filter's seeds (`due_to` prefix
+  `analyst-rule`), recursion gate (`triggered_by == "Rule"`), body-predicate
+  walk over `clause_sets`, and keep-index over `(label, term)` are all
+  functions of the canonical multiset only,
+- secondary-filter (`label_filtering` / `workflow_filtering` /
+  `analyst_filtering`) parity, given Tier 2 below.
+
+The record multiset decomposes into two families, each independently checkable:
+
+**Fact records** — deterministic re-assertion schedule (verified against real
+traces; a consequence of `persistent=False` worlds resetting to `[0,1]` each
+step):
+
+| Source | Records emitted |
+|---|---|
+| static fact (incl. every `hasLabel` workflow fact) | one per `t ∈ [0, END_TIME]`, `due_to` = fact name |
+| timed fact on `[t0, t1]` (`initial-control`, `workflow-edge-i`) | one per `t ∈ [t0, t1]`, `due_to` = fact name |
+| GraphML attribute (KG nodes/edges, e.g. `can_cause`) | one per `t ∈ [0, END_TIME]`, `due_to = "graph-attribute-fact"` |
+
+All fact records: `triggered_by = "Fact"`, `clause_sets = ()`,
+`consistent = True`.
+
+**Rule records** — by §5, within scope each `(rule, head-grounding, t)` fires
+at most once, and its clause sets are the *complete* qualified-grounding sets
+at `t`, uniquely determined by the inputs. So the expected rule-record multiset
+is: for every analyst rule `r`, head grounding `h`, and timestep `t+1 ≤
+END_TIME` such that `r`'s body is satisfied at `t` (all five clauses have a
+consistent grounding meeting their interval thresholds, `analystAt` read
+closed-world), exactly one record
+
+```
+(t+1, "analystAt", Node(h), name(r), "Rule", True,
+ (Q₁, Q₂, Q₃, Q₄, Q₅))
+```
+
+where `Qᵢ` is the full set of groundings of clause `i` qualified at `t` **in
+the rule-consistent join** (the sets PyReason's `atom_trace` records: every
+grounding that participates in some satisfying assignment, not only the
+ARG-MAX winner). Recording only the winning witness is a contract violation —
+`base_filter`'s transitive walk visits *every* grounding in every clause set.
+
+## 4. Tier 2 — bounds (REQUIRED, order-tolerant)
+
+Per key `(label, term, time)`:
+
+1. **Final bound — exact.** The last `new_bound` after all updates at that key
+   must be equal across engines. For `analystAt` keys this is precisely the
+   temporal interval map already validated by `validate_minimal_parity.py`.
+   For fact keys it is the fact's bound (`[1,1]`).
+2. **Chain consistency — per engine (self-check).** Within one engine's
+   ordered records for a key: the first `old_bound` is the reset value
+   `[0,1]`; each subsequent `old_bound` equals the previous `new_bound`; the
+   last `new_bound` is the final bound.
+3. **Interleaving — NOT compared.** When ≥ 2 records share a key (two analyst
+   rules deriving the same head at the same t), the sequence of intermediate
+   `old_bound → new_bound` transitions is engine-order-dependent and is
+   excluded from comparison. (Consequence of interval intersection being
+   commutative/associative: the final bound is order-free; the intermediates
+   are not.) No downstream consumer reads intermediates: `base_filter` never
+   touches bounds; `workflow_filtering` reads only `new_bound[1]` of
+   `stepFrom` records, which are single-record fact keys.
+4. **Float equality** = equality of IEEE-754 float32 bit patterns
+   (`float32_to_u32`) after parsing; the PyReason side parses the CSV decimal
+   strings to float64 first. This matches the digest convention already used
+   by `benchmark_srdatalog.py`.
+
+The annotation semantics behind rule-record bounds (already implemented and
+value-validated, restated here as the normative definition): per firing, each
+satisfying body grounding is a witness; a witness's candidate interval is
+`[min, min]-pairing` per `paired_minimum_bounds_ann_fn`; the firing's
+contributed interval is that of the witness with maximal lower bound, ties
+broken by **least admission rank** (PyReason first-match); the world update is
+`old_bound ∩ contributed`.
+
+## 5. Why no chronology is needed (the snapshot-stability argument)
+
+The PR's conversion report declines to reproduce "callback trace chronology"
+— same-snapshot witness groups and global `Fixed-Point-Operation` numbers.
+Within the scoped fragment this problem dissolves:
+
+- **Lemma 1 (no intra-timestep feedback).** Every in-scope rule carries delay
+  `<-1`: bodies are evaluated against the state at `t`, heads land at `t+1`.
+  The state at `t` is fully determined before any rule evaluation at `t`
+  begins — it consists of fact assertions scheduled at `t` (§3 table) and
+  delayed heads computed from `t-1`. No in-scope derivation can change a set
+  another in-scope body reads at the same `t`.
+- **Lemma 2 (stable qualified sets).** Therefore the qualified set `Qᵢ` of
+  every clause at `(rule, head, t)` is the unique fixpoint-independent set
+  determined by the inputs — there is no "growing snapshot" across
+  iterations. (The multi-row-per-key rows observed in full-VulReasoner traces
+  are caused by `<-0` label rules growing `hasLabel` within a timestep —
+  excluded from scope.)
+- **Corollary.** Each `(rule, head, t)` yields at most one record, computable
+  without replaying PyReason's operational loop. The trace is a pure function
+  of the inputs.
+
+This is why `Fixed-Point-Operation` is excluded (§7): it is the only trace
+column whose value is chronology, and nothing consumes it.
+
+## 6. Derived-output requirements
+
+For the per-KG result shape (`run_reasoning_for_kg`):
+
+| Field | Requirement |
+|---|---|
+| `input_valid` | `True` on both engines (no inconsistency sources in scope); any `consistent = False` record is a contract violation, not a tolerated difference |
+| `num_inferences` | equal (follows from Tier 1) |
+| `reasoning_trace` (base-filtered) | equal as canonical multisets (follows from Tiers 1–2) |
+| `loaded_rules` | the six analyst rules, parsed per `parse_rules_from_file`, in file order — required because `base_filter` maps `due_to` → body predicates through it |
+| `metrics`, `fixed_point_operation` | excluded (§7) |
+
+## 7. Explicitly out of contract
+
+- `Fixed-Point-Operation` values (SRDatalog may synthesize any int, e.g. `0`
+  or a per-time counter; must still be parseable as int).
+- Row **order** in CSVs / JSON arrays, and ordering inside clause cells.
+  Comparison is multiset-based after canonicalization; byte-identical output
+  is a non-goal. (If byte-stable artifacts are wanted later, apply one shared
+  normalizer — sorted records, sorted clause sets — to *both* engines'
+  outputs; do not chase PyReason's native ordering.)
+- Trace CSV filenames/timestamps, edge-vs-node file column counts, float
+  *formatting* (only float32 values are compared).
+- Intermediate `old_bound → new_bound` interleavings on multi-record keys
+  (§4.3).
+- Everything in §1 "Excluded".
+
+## 8. Conformance procedure
+
+A conforming implementation is verified by a differential harness
+(`validate_trace_parity.py`, companion to `validate_minimal_parity.py`):
+
+1. **Oracle:** run the minimal example under PyReason, `pr.save_rule_trace`,
+   load CSVs with `trace_conversion` semantics, canonicalize per §2.
+2. **Candidate:** run the SRDatalog implementation; emit records per §3 (fact
+   schedule from the input manifest; rule records from the materialized
+   candidate/selected relations plus clause-set queries), canonicalize per §2.
+3. **Compare:** (a) Tier-1 multiset equality — report missing / extra records
+   grouped by key; (b) Tier-2 final-bound map equality under float32 bit
+   equality; (c) chain self-checks per engine; (d) run `base_filter` +
+   secondary filters over both canonical traces and assert equal kept
+   multisets — this guards the theorem-level claims in §3 empirically.
+4. **Pass** = all of (a)–(d) on: the checked-in `CWE_121_MVP2` workflow, and
+   the deterministic stress workloads of `stress_workload.py` at ≥ 2 sizes.
+
+Divergence triage order: a Tier-1 mismatch on *fact* records is an ingest/
+schedule bug; on *rule* records with equal clause sets it is a threshold/CWA
+read bug; a clause-set mismatch is a qualified-set (not winner-only)
+materialization bug; a Tier-2-only mismatch is an annotation-fn or
+intersection bug.
+
+## 9. Versioning
+
+This is **v1**, scoped to §1. Any widening — `<-0` rules, negation/
+`inconsistent_rule`, `set_static`, persistence, `obs` — must be a new
+contract version with its own stability argument replacing §5 (Lemma 1 fails
+for `<-0` rules and for the undelayed `inconsistent_rule`; conflict repair
+additionally breaks §4.3's commutativity argument).
diff --git a/minimal_vulreasoner/run_vr_phase2.py b/minimal_vulreasoner/run_vr_phase2.py
new file mode 100644
index 0000000..e28ba70
--- /dev/null
+++ b/minimal_vulreasoner/run_vr_phase2.py
@@ -0,0 +1,389 @@
+#!/usr/bin/env python3
+'''Run one real VulReasoner trajectory's phase-2 fragment on SRDatalog.
+
+Hybrid step-4 runner (see ~/Projects/HANDOFF.md and TRACE_PARITY_CONTRACT.md):
+consumes a phase-2 input JSON extracted from a /reason capture
+({initial_node, edges, end_time, has_label:[[entity,label,lo,hi],...]}),
+the CWE_121_MVP2 GraphML, and the six analyst rules; runs the GPU fixpoint;
+prints RESULT_JSON with:
+  - analyst_rows: the temporal analystAt map {node@time: [lower, upper]}
+  - witnesses: per analyst rule, every satisfying body grounding
+    [cb2, next_time, cb1, cause_label, effect_label] (full qualified sets per
+    contract Tier 1, not the ARG-MAX winner only)
+  - tc_facts: connector facts derived by native SRDatalog transitive closure
+    (kg_property_rules semantics: can_cause/contributes_to/derives, [1,1])
+
+Connector transitivity is native SRDatalog TC via per-predicate Closed
+relations; base connector facts are asserted [1,1] at ingest (true for this
+KG), so TC rows inherit first-hop rank/bounds and still read [1,1].
+
+Usage (from the srdatalog repo root):
+  uv run --project minimal_vulreasoner --frozen \
+    python minimal_vulreasoner/run_vr_phase2.py --inputs t0.json [--no-compile]
+'''
+
+from __future__ import annotations
+
+import argparse
+import json
+import os
+import sys
+import time
+from pathlib import Path
+
+REPO_SRC = Path(__file__).resolve().parents[1] / "src"
+if str(REPO_SRC) not in sys.path:
+  sys.path.insert(0, str(REPO_SRC))
+HERE = Path(__file__).resolve().parent
+if str(HERE) not in sys.path:
+  sys.path.insert(0, str(HERE))
+
+import csv
+
+from srdatalog import (
+  Program,
+  Relation,
+  Var,
+  build_project,
+  compile_jit_project,
+  float32_to_u32,
+  interval_lattice,
+  max_lower_lattice,
+)
+from srdatalog.dsl import Filter, Let
+from stress_workload import decode_float32_bits
+
+from benchmark_srdatalog import _bind, _compiler_config
+from example_config import KG_FILE, RULES_FILE
+from graphml_ingest import parse_graphml
+from srdatalog_query import _minimum3
+from analyst_rule_loader import load_analyst_rules
+
+import ctypes  # noqa: E402  (after _bind import for parity with peers)
+
+# kg_property_rules.csv transitive predicates that are also analyst connectors.
+TRANSITIVE_CONNECTORS = frozenset({"can_cause", "contributes_to", "derives"})
+
+
+def emit_trajectory_dataset(inputs: dict, output_dir: Path, rule_specs,
+                            kg_file=KG_FILE) -> dict:
+  '''Emit the extensional relations for one real trajectory.'''
+  connector_predicates = tuple(spec.connector_predicate for spec in rule_specs)
+  graph = parse_graphml(kg_file, connector_predicates=connector_predicates)
+  bad = [c for c in graph.connectors if (c.lower, c.upper) != (1.0, 1.0)]
+  if bad:
+    raise ValueError(
+      f"TC inheritance assumes [1,1] base connector facts; found {bad[:3]}"
+    )
+
+  blocks = {inputs["initial_node"]}
+  for src, dst in inputs["edges"]:
+    blocks.add(src)
+    blocks.add(dst)
+  labels = {label for _, label, _, _ in inputs["has_label"]}
+  entities = {entity for entity, _, _, _ in inputs["has_label"]}
+  symbols = sorted(set(graph.nodes) | blocks | labels | entities)
+  symbol_ids = {symbol: index for index, symbol in enumerate(symbols)}
+  one = float32_to_u32(1.0)
+
+  output_dir.mkdir(parents=True, exist_ok=True)
+
+  def write(name, rows):
+    with (output_dir / name).open("w", newline="") as handle:
+      csv.writer(handle).writerows(rows)
+
+  # PyReason initial-control Fact is valid on inclusive [0, 1] at [1,1].
+  write("analyst_seed.csv",
+        ((symbol_ids[inputs["initial_node"]], t, one, one) for t in (0, 1)))
+  # Static hasLabel facts with augmenter bounds (timeless = static).
+  write("has_label.csv",
+        ((symbol_ids[e], symbol_ids[l], float32_to_u32(lo), float32_to_u32(hi))
+         for e, l, lo, hi in inputs["has_label"]))
+  # PyReason asserts workflow edge i on inclusive times [i+1, i+2].
+  step_rows = []
+  for index, (src, dst) in enumerate(inputs["edges"]):
+    for t in (index + 1, index + 2):
+      step_rows.append((symbol_ids[src], symbol_ids[dst], t))
+  write("step_from.csv", step_rows)
+  write("successor.csv", ((t, t + 1) for t in range(inputs["end_time"])))
+
+  by_predicate = {predicate: [] for predicate in connector_predicates}
+  for fact in graph.connectors:
+    by_predicate[fact.predicate].append(fact)
+  for predicate, facts in by_predicate.items():
+    write(f"{predicate}.csv",
+          ((symbol_ids[f.source], symbol_ids[f.target], f.rank,
+            float32_to_u32(f.lower), float32_to_u32(f.upper)) for f in facts))
+
+  return {
+    "symbols": symbol_ids,
+    "graph_nodes": len(graph.nodes),
+    "graph_edges": graph.edge_count,
+    "selected_connector_facts": len(graph.connectors),
+    "base_connector_pairs": {
+      predicate: sorted({(f.source, f.target) for f in facts})
+      for predicate, facts in by_predicate.items()
+    },
+  }
+
+
+def build_phase2_program(rule_specs) -> Program:
+  '''srdatalog_query.build_analyst_program plus native TC + witness outputs.'''
+  if any(spec.delay != 1 for spec in rule_specs):
+    raise ValueError("the explicit Successor encoding currently supports only <-1")
+  if any(spec.annotation_function != "paired_minimum_bounds_ann_fn"
+         for spec in rule_specs):
+    raise ValueError("unsupported analyst annotation function")
+
+  analyst_seed = Relation("AnalystSeed", 4, column_types=(int,) * 4,
+                          input_file="analyst_seed.csv")
+  has_label = Relation("HasLabel", 4, column_types=(int,) * 4,
+                       input_file="has_label.csv")
+  step_from = Relation("StepFrom", 3, column_types=(int,) * 3,
+                       input_file="step_from.csv")
+  successor = Relation("Successor", 2, column_types=(int,) * 2,
+                       input_file="successor.csv")
+  analyst_at = Relation(
+    "AnalystAt", 4, column_types=(int,) * 4, print_size=True,
+    output_file="analyst_at.csv",
+    value_spec=interval_lattice(key_columns=(0, 1), lower_column=2, upper_column=3),
+  )
+
+  base_relations = {}
+  joined_relations = {}
+  rules = []
+  tcx, tcy, tcz = Var("tcx"), Var("tcy"), Var("tcz")
+  tcr1, tcl1, tcu1 = Var("tcr1"), Var("tcl1"), Var("tcu1")
+  tcr2, tcl2, tcu2 = Var("tcr2"), Var("tcl2"), Var("tcu2")
+  for spec in rule_specs:
+    base = Relation(spec.relation_name, 5, column_types=(int,) * 5,
+                    input_file=spec.input_file)
+    base_relations[spec.connector_predicate] = base
+    if spec.connector_predicate in TRANSITIVE_CONNECTORS:
+      closed = Relation(f"{spec.relation_name}Closed", 5, column_types=(int,) * 5,
+                        print_size=True)
+      rules.append(
+        (closed(tcx, tcy, tcr1, tcl1, tcu1)
+         <= base(tcx, tcy, tcr1, tcl1, tcu1)).named(f"Copy{spec.relation_name}"))
+      # kg_property_rules transitivity; [1,1] inherited from the first hop
+      # (asserted at ingest), rank likewise — witness selection is unaffected
+      # because every derived interval is identical.
+      rules.append(
+        (closed(tcx, tcz, tcr1, tcl1, tcu1)
+         <= closed(tcx, tcy, tcr1, tcl1, tcu1)
+         & closed(tcy, tcz, tcr2, tcl2, tcu2)).named(f"TC{spec.relation_name}"))
+      joined_relations[spec.connector_predicate] = closed
+    else:
+      joined_relations[spec.connector_predicate] = base
+
+  cb1, cb2 = Var("cb1"), Var("cb2")
+  time_, next_time = Var("time"), Var("next_time")
+  cause_label, effect_label = Var("cause_label"), Var("effect_label")
+  analyst_lower, analyst_upper = Var("analyst_lower"), Var("analyst_upper")
+  cause_lower, cause_upper = Var("cause_lower"), Var("cause_upper")
+  effect_lower, effect_upper = Var("effect_lower"), Var("effect_upper")
+  connector_lower, connector_upper = Var("connector_lower"), Var("connector_upper")
+  connector_rank = Var("connector_rank")
+  result_lower, result_upper = Var("result_lower"), Var("result_upper")
+
+  rules.append(
+    (analyst_at(cb1, time_, analyst_lower, analyst_upper)
+     <= analyst_seed(cb1, time_, analyst_lower, analyst_upper)).named("AnalystSeed"))
+
+  witness_relations = {}
+  for spec in rule_specs:
+    connector = joined_relations[spec.connector_predicate]
+    candidate = Relation(
+      f"{spec.relation_name}Candidate", 5, column_types=(int,) * 5,
+      value_spec=max_lower_lattice(key_columns=(0, 1), rank_column=2,
+                                   lower_column=3, upper_column=4),
+    )
+    witness = Relation(f"{spec.relation_name}Witness", 5, column_types=(int,) * 5,
+                       print_size=True)
+    witness_relations[spec.name] = witness
+
+    def body():
+      return (
+        analyst_at(cb1, time_, analyst_lower, analyst_upper)
+        & has_label(cb1, cause_label, cause_lower, cause_upper)
+        & has_label(cb2, effect_label, effect_lower, effect_upper)
+        & connector(cause_label, effect_label, connector_rank,
+                    connector_lower, connector_upper)
+        & step_from(cb1, cb2, time_)
+        & successor(time_, next_time)
+        & Filter(
+          vars=(analyst_lower.name, analyst_upper.name,
+                cause_lower.name, cause_upper.name,
+                effect_lower.name, effect_upper.name,
+                connector_lower.name, connector_upper.name),
+          code=(
+            f"return {analyst_lower.name} >= {float32_to_u32(spec.analyst_bound.lower)} && "
+            f"{analyst_upper.name} <= {float32_to_u32(spec.analyst_bound.upper)} && "
+            f"{cause_lower.name} >= {float32_to_u32(spec.cause_label_bound.lower)} && "
+            f"{cause_upper.name} <= {float32_to_u32(spec.cause_label_bound.upper)} && "
+            f"{effect_lower.name} >= {float32_to_u32(spec.effect_label_bound.lower)} && "
+            f"{effect_upper.name} <= {float32_to_u32(spec.effect_label_bound.upper)} && "
+            f"{connector_lower.name} >= {float32_to_u32(spec.connector_bound.lower)} && "
+            f"{connector_upper.name} <= {float32_to_u32(spec.connector_bound.upper)};"
+          ),
+        )
+        & Let(result_lower.name,
+              _minimum3(cause_lower.name, effect_lower.name, connector_lower.name),
+              deps=(cause_lower.name, effect_lower.name, connector_lower.name))
+        & Let(result_upper.name,
+              _minimum3(cause_upper.name, effect_upper.name, connector_upper.name),
+              deps=(cause_upper.name, effect_upper.name, connector_upper.name))
+      )
+
+    rules.append(
+      (candidate(cb2, next_time, connector_rank, result_lower, result_upper)
+       <= body()).named(f"Analyst{spec.relation_name}"))
+    # Full qualified groundings for contract Tier 1 — every satisfying body
+    # assignment, independent of the candidate ARG-MAX selection.
+    rules.append(
+      (witness(cb2, next_time, cb1, cause_label, effect_label)
+       <= body()).named(f"Witness{spec.relation_name}"))
+    rules.append(
+      (analyst_at(cb2, next_time, result_lower, result_upper)
+       <= candidate(cb2, next_time, connector_rank, result_lower, result_upper)
+       ).named(f"Promote{spec.relation_name}Candidate"))
+
+  return Program(rules=rules), witness_relations
+
+
+def _copy_rows(lib, name: str, columns: int):
+  import cupy as cp
+  count = int(lib.srdatalog_dev_count(name.encode()))
+  host = []
+  for column in range(columns):
+    pointer = int(lib.srdatalog_dev_ptr(name.encode(), column))
+    memory = cp.cuda.UnownedMemory(pointer, count * 4, lib)
+    device = cp.ndarray((count,), dtype=cp.uint32,
+                        memptr=cp.cuda.MemoryPointer(memory, 0))
+    host.append(device.get())
+  cp.cuda.get_current_stream().synchronize()
+  return [tuple(int(host[c][row]) for c in range(columns)) for row in range(count)]
+
+
+def main() -> None:
+  parser = argparse.ArgumentParser()
+  parser.add_argument("--inputs", required=True, help="phase-2 input JSON")
+  parser.add_argument("--kg", default=str(KG_FILE),
+                      help="GraphML KG to ingest connectors from (default: the "
+                           "minimal example's CWE_121_MVP2 copy)")
+  parser.add_argument("--end-time", type=int, default=None,
+                      help="override the input JSON's end_time (sizes the "
+                           "successor relation)")
+  parser.add_argument("--cache-base", default="./build")
+  parser.add_argument("--data-dir", default=None)
+  parser.add_argument("--jobs", type=int, default=8)
+  parser.add_argument("--no-compile", action="store_true")
+  parser.add_argument("--repeat", type=int, default=1,
+                      help="extra srdatalog_run calls after the first (the "
+                           "first pays GPU/RMM init; repeats measure cached "
+                           "execution, same convention as benchmark_srdatalog)")
+  args = parser.parse_args()
+
+  inputs = json.loads(Path(args.inputs).read_text())
+  if args.end_time is not None:
+    inputs["end_time"] = args.end_time
+  rule_specs = load_analyst_rules(RULES_FILE)
+  data_dir = Path(args.data_dir or f"./build/vr_phase2_data_t{inputs.get('trajectory', 'x')}")
+
+  ingest_started = time.perf_counter()
+  manifest = emit_trajectory_dataset(inputs, data_dir, rule_specs,
+                                     kg_file=Path(args.kg))
+  ingest_seconds = time.perf_counter() - ingest_started
+  symbol_names = {sid: name for name, sid in manifest["symbols"].items()}
+
+  program, witness_relations = build_phase2_program(rule_specs)
+  emit_started = time.perf_counter()
+  project = build_project(program, "VulReasonerPhase2Plan", cache_base=args.cache_base)
+  emit_seconds = time.perf_counter() - emit_started
+
+  compile_seconds = 0.0
+  if args.no_compile:
+    artifacts = list(Path(project["dir"]).glob("*.so"))
+    if not artifacts:
+      raise RuntimeError(f"no cached shared library in {project['dir']}; omit --no-compile")
+    artifact = str(artifacts[0].resolve())
+  else:
+    started = time.perf_counter()
+    build = compile_jit_project(project, _compiler_config(args.jobs))
+    compile_seconds = time.perf_counter() - started
+    if not build.ok():
+      failure = next(r for r in build.compile_results if r.returncode)
+      raise RuntimeError((failure.stderr or failure.stdout)[-12000:])
+    artifact = str(Path(build.artifact).resolve())
+
+  lib = _bind(artifact)
+  if lib.srdatalog_init() != 0:
+    raise RuntimeError("srdatalog_init failed")
+  load_started = time.perf_counter()
+  if lib.srdatalog_load_all(str(data_dir.resolve()).encode()) != 0:
+    raise RuntimeError("srdatalog_load_all failed")
+  load_seconds = time.perf_counter() - load_started
+  run_seconds_all = []
+  for _ in range(max(1, args.repeat)):
+    run_started = time.perf_counter()
+    if lib.srdatalog_run(0) != 0:
+      raise RuntimeError("srdatalog_run failed")
+    run_seconds_all.append(time.perf_counter() - run_started)
+  run_seconds = run_seconds_all[0]
+
+  raw = _copy_rows(lib, "AnalystAt", 4)
+  analyst_rows = dict(sorted(
+    (f"{symbol_names[node]}@{t}", [decode_float32_bits(lo), decode_float32_bits(hi)])
+    for node, t, lo, hi in raw))
+
+  witnesses = {}
+  for rule_name, relation in witness_relations.items():
+    rows = _copy_rows(lib, relation.name, 5)
+    witnesses[rule_name] = sorted(
+      [symbol_names[cb2], t, symbol_names[cb1],
+       symbol_names[cause], symbol_names[effect]]
+      for cb2, t, cb1, cause, effect in rows)
+
+  tc_facts = {}
+  for spec in rule_specs:
+    if spec.connector_predicate not in TRANSITIVE_CONNECTORS:
+      continue
+    rows = _copy_rows(lib, f"{spec.relation_name}Closed", 5)
+    base_pairs = set(map(tuple, manifest["base_connector_pairs"][spec.connector_predicate]))
+    derived = sorted(
+      {(symbol_names[x], symbol_names[y]) for x, y, _, _, _ in rows}
+      - base_pairs)
+    tc_facts[spec.connector_predicate] = {
+      "derived_pairs": [list(p) for p in derived],
+      "derived_bounds": sorted({
+        (decode_float32_bits(lo), decode_float32_bits(hi))
+        for x, y, _, lo, hi in rows
+        if (symbol_names[x], symbol_names[y]) not in base_pairs}),
+    }
+
+  result = {
+    "engine": "srdatalog",
+    "trajectory": inputs.get("trajectory"),
+    "graph_nodes": manifest["graph_nodes"],
+    "graph_edges": manifest["graph_edges"],
+    "selected_connector_facts": manifest["selected_connector_facts"],
+    "analyst_rows": analyst_rows,
+    "witnesses": witnesses,
+    "tc_facts": tc_facts,
+    "ingest_seconds": ingest_seconds,
+    "emit_seconds": emit_seconds,
+    "compile_seconds": compile_seconds,
+    "load_seconds": load_seconds,
+    "run_seconds": run_seconds,
+    "run_seconds_all": run_seconds_all,
+  }
+  print("RESULT_JSON=" + json.dumps(result, sort_keys=True), flush=True)
+  lib.srdatalog_shutdown()
+  sys.stdout.flush()
+  sys.stderr.flush()
+  # Same ctypes/CUDA teardown-order caveat as run_srdatalog_reasoner.py.
+  os._exit(0)
+
+
+if __name__ == "__main__":
+  main()