fix(elf): keep program header table intact through eu-strip

[littledivy]

Problem

deno compile binaries built inside a flatpak sandbox segfault at startup (exit 139) since Deno 2.9 — denoland/deno#35633. Bisected to libsui 0.16.0 (the in-place Elf::append from #72).

Root cause

Elf::append relocates the program header table past the original EOF, into the file gap just before the appended note. flatpak-builder runs eu-strip (elfutils), which lays the stripped output out itself with ELF_F_LAYOUT and zero-fills every file gap that falls between two allocated sections. With only a note-sized .note.sui section past that gap, eu-strip treats the relocated program header table as dead space and zeroes it → all-NULL program headers → segfault on exec.

Reproduced directly with deno 2.9.0 on Linux: compiled binary → eu-strip → 14 NULL program headers, exit 139.

Two other theories were ruled out empirically:

• Dropping the .note.sui section stops the crash but eu-strip then discards the unbacked note → "Could not find standalone binary section" (payload lost).
• The discontiguous high PT_LOAD is not the trigger — patchelf produces the same layout and survives eu-strip; the deciding factor is whether the phdr table is covered by an allocated section.

Fix

Cover the relocated program header table with its own allocated .sui.phdrs (SHT_PROGBITS) section so section-based strip tools that preserve the byte layout keep it. It has to be a separate PROGBITS section rather than folding the bytes into .note.sui: BFD strip parses SHT_NOTE contents, so a note section spanning the (non-note) program header bytes corrupts the note and loses it on strip. .note.sui keeps covering only the note; the runtime still discovers it via its PT_NOTE program header.

Test

Adds test_elf_note_survives_eu_strip: appends a note, runs eu-strip, and asserts the program header table is not zeroed, the note still round-trips, and the stripped binary still executes (skips gracefully if eu-strip is absent). Updates test_elf_append_preserves_original_bytes for the extra section header.

Verified on Linux (elfutils 0.190): before — segfault; after — runs, phdrs intact, payload found. test_elf_note_survives_strip (BFD strip) still passes.

Note: BFD strip still breaks exec on these binaries, but that is pre-existing (0.16.0 behaves the same) and flatpak uses eu-strip.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.74%. Comparing base (307b58c) to head (abc271f).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #75      +/-   ##
==========================================
+ Coverage   72.00%   72.74%   +0.73%     
==========================================
  Files           3        3              
  Lines        1036     1064      +28     
==========================================
+ Hits          746      774      +28     
  Misses        290      290              

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