fix(install): bridge system/ → .hex/ for v0.16+ binary; revert premature .legacy rename

[arrra]

Summary

The v0.16.0 release ("Real-port phase complete") introduced two regressions that break a fresh install:

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). But install.sh copies foundation's system/* into \$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 on a fresh install with:

   python3: can't open file '/<install>/system/skills/memory/scripts/memory_index.py': [Errno 2] No such file or directory
   bash: /<install>/system/scripts/hex-doctor: No such file or directory
   

2. Premature .legacy quarantine. memory_index, memory_search, and startup were renamed to .legacy.* but they are still invoked at runtime:
   • hex memory index|search shells out to memory_index.py / memory_search.py (Rust subcommand is a wrapper, not a port).
   • The Memory System section in this repo's CLAUDE.md and system/skills/memory/SKILL.md both still document the non-.legacy paths.
   • system/skills/hex-startup/SKILL.md runs \$HEX_DIR/.hex/scripts/startup.sh.

Changes

• install.sh: add ln -sfn .hex \"\$TARGET_DIR/system\" alongside the existing .agents/skills → .hex/skills symlink. Same pattern, additive fix.
• Rename system/skills/memory/scripts/memory_index.legacy.py → memory_index.py
• Rename system/skills/memory/scripts/memory_search.legacy.py → memory_search.py
• Rename system/scripts/startup.legacy.sh → startup.sh

Total: 4 files changed, 7 insertions(+).

Test plan

Verified on a real install (workspace at `/Users/sagarsingh/hex`, hex 0.8.0 commit 9412f85):

• Reproduced both failure modes (hex memory index, hex doctor --smoke, missing startup.sh) before applying the fix
• Applied the equivalent symlinks locally (without modifying upstream files) and confirmed:
  • hex memory index → Done in 0.02s: 0 indexed, 327 unchanged, 0 removed
  • hex doctor --smoke --quiet → runs to completion (1 unrelated warning)
  • which hex → resolves via \$HEX_DIR/.hex/bin/hex
  • bash \$HEX_DIR/.hex/scripts/startup.sh → runs the legacy script transparently
• Reviewer should run bash install.sh /tmp/hex-test on a clean dir to verify install lays out correctly
• Reviewer should run cd /tmp/hex-test && \$PWD/.hex/bin/hex memory index to verify the binary resolves the new symlink

Notes

• Discovered while running /hex-upgrade then /hex-startup post-v0.16.0 upgrade. Standing Order S1 ("sync fixes to hex base") motivated upstreaming.
• Alternative fixes considered:
  • Patch the Rust binary's path resolver to look at .hex/... (correct but requires re-release).
  • Change install.sh to copy system/* to \$TARGET_DIR/system/* instead of .hex/* (more invasive — breaks every existing instance's directory expectations).
• This minimal-symlink approach matches the existing .agents/skills pattern and is fully reversible.

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