fix: preserve file modes during template substitution

[alloutflo]

Summary

• preserve each template file's original mode on the temporary file before the atomic rename
• keep the source InstallEngine.ts and shipped skill copy synchronized
• add a Bun regression test proving an executable hook remains executable after substitution

Closes #1803

Root cause

substituteTree() wrote replacement content to a new temporary inode. That inode inherited the process umask (typically 0644), and the subsequent rename replaced the executable source file together with its mode.

Validation

• bun test LifeOS/test/skills/LifeOS/Tools/InstallEngine.test.ts — 1 passed
• bun build LifeOS/Tools/InstallEngine.ts --target=bun — successful
• verified both distributed InstallEngine.ts copies are byte-identical
• git diff --check