From 5267dc81893fa1d6488fdfe777946de463aa30d4 Mon Sep 17 00:00:00 2001
From: Sagar Singh <ssing128@gmail.com>
Date: Tue, 19 May 2026 15:48:07 -0700
Subject: [PATCH] =?UTF-8?q?fix(install):=20bridge=20system/=20=E2=86=92=20?=
 =?UTF-8?q?.hex/=20for=20v0.16+=20binary;=20revert=20premature=20.legacy?=
 =?UTF-8?q?=20rename?=
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The v0.16.0 release ("Real-port phase complete") renamed three actively-used
scripts to `.legacy` AND assumes a layout the install.sh does not produce.
Two separate bugs in one release:

1. **Layout mismatch.** The Rust `hex` binary has hardcoded path constants
   that prefix `system/skills/...` and `system/scripts/...` (verified via
   `strings system/scripts/bin/hex`). install.sh copies foundation's
   `system/*` to `$TARGET_DIR/.hex/*` and never creates a `system/` entry
   at the install root — so `hex memory index/search`, `hex doctor`, and
   `hex integration` all fail with `No such file or directory` on a fresh
   install. Add `ln -sfn .hex "$TARGET_DIR/system"` alongside the existing
   `.agents/skills → .hex/skills` symlink. Same pattern, additive fix.

2. **Premature `.legacy` quarantine.** memory_index, memory_search, and
   startup are not legacy — they are still invoked at runtime:
   - `hex memory index|search` shells out to memory_index.py/memory_search.py
     (the Rust subcommand is a wrapper, not a port).
   - SKILL.md (Memory System section) and the foundation CLAUDE.md memory
     instructions both reference the non-`.legacy` paths.
   - hex-startup SKILL.md runs `.hex/scripts/startup.sh`.
   Rename them back to canonical names so existing tooling and the binary
   both find them.

Verified on a real install (Sagar's hex instance): with this branch applied
locally via symlinks, `hex memory index` indexes 327 files cleanly,
`hex doctor --smoke` runs to completion, and `startup.sh` is resolvable.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---
 install.sh                                                 | 7 +++++++
 system/scripts/{startup.legacy.sh => startup.sh}           | 0
 .../scripts/{memory_index.legacy.py => memory_index.py}    | 0
 .../scripts/{memory_search.legacy.py => memory_search.py}  | 0
 4 files changed, 7 insertions(+)
 rename system/scripts/{startup.legacy.sh => startup.sh} (100%)
 rename system/skills/memory/scripts/{memory_index.legacy.py => memory_index.py} (100%)
 rename system/skills/memory/scripts/{memory_search.legacy.py => memory_search.py} (100%)

diff --git a/install.sh b/install.sh
index ede09b2..a228a0a 100755
--- a/install.sh
+++ b/install.sh
@@ -141,6 +141,13 @@ fi
 mkdir -p "$TARGET_DIR/.agents"
 ln -sfn ../.hex/skills "$TARGET_DIR/.agents/skills"
 
+# Symlink system/ → .hex/ so the hex Rust binary (v0.16+) resolves its hardcoded
+# "system/skills/...", "system/scripts/..." paths against the install layout.
+# Without this, `hex memory index/search`, `hex doctor`, and `hex integration`
+# all fail with "No such file or directory" because the binary's path resolver
+# was built against the foundation source-tree layout, not the install layout.
+ln -sfn .hex "$TARGET_DIR/system"
+
 # Seed optional configs doctor expects. Defaults are safe and overridable later.
 echo '{}' > "$TARGET_DIR/.hex/settings.json"
 
diff --git a/system/scripts/startup.legacy.sh b/system/scripts/startup.sh
similarity index 100%
rename from system/scripts/startup.legacy.sh
rename to system/scripts/startup.sh
diff --git a/system/skills/memory/scripts/memory_index.legacy.py b/system/skills/memory/scripts/memory_index.py
similarity index 100%
rename from system/skills/memory/scripts/memory_index.legacy.py
rename to system/skills/memory/scripts/memory_index.py
diff --git a/system/skills/memory/scripts/memory_search.legacy.py b/system/skills/memory/scripts/memory_search.py
similarity index 100%
rename from system/skills/memory/scripts/memory_search.legacy.py
rename to system/skills/memory/scripts/memory_search.py