emrg: packaging: fix bundled python venv (pyvenv.cfg home) via bin/python wrapper

[how2how2how2-arch]

Fixes the bundled-Python venv breakage reported in the rant below.

Rant (verbatim)

install 打包 Python 创建的 venv 不可用（pyvenv.cfg home 路径错误），任务无法安装科研依赖

~/.emrg/install/bin/python（Python 3.13.9）执行 python -m venv <dir> 生成的 pyvenv.cfg 中 home = ~/.emrg/install/bin，但解释器实际位于 ~/.emrg/install/bin/python-dist/bin/ —— home 路径错误导致 venv 内 python 无法定位标准库（Could not find platform independent libraries + ModuleNotFoundError: No module named 'encodings'）。

Root cause

packaging/build-runtime.sh (R82) installs bin/python as a symlink → python-dist/bin/python3.13. When invoked through the symlink, CPython keeps sys.executable = <install>/bin/python (the symlink path) while sys.prefix correctly resolves to <install>/bin/python-dist. python -m venv derives pyvenv.cfg home from dirname(sys._base_executable) → <install>/bin, and the venv base-executable recompute does not follow the symlink → the venv python cannot find the stdlib. Any emrg task creating a venv (journal/paper/open-source) fails to pip install numpy/scipy/ILP.

Reproduced locally on the real install bundle: symlink invocation → home = .../install/bin, venv python dies with No module named 'encodings'; manual pyvenv.cfg fix per the rant works.

Fix

1. packaging/assets/python-wrapper.sh (new): POSIX wrapper that exec's the real interpreter $(dirname $0)/python-dist/bin/python3.13 so sys.executable resolves to the real path → venv writes the correct home = .../python-dist/bin.
2. packaging/build-runtime.sh: POSIX branch now copies the wrapper to bin/python + bin/python3 instead of creating symlinks (Windows unchanged — it already uses the python-dist exe directly).
3. packaging/smoke-test.sh: new item 14 — regression smoke that creates a venv with the bundled python, imports encodings, and checks pip (runs in build-release CI against the real built artifact; Windows uses the python-dist exe + Scripts/ layout).

Verification

• Wrapper end-to-end (faithful layout, real bundle): sys.executable = real path; pyvenv.cfg home = .../python-dist/bin; venv import encodings OK; pip 25.2 present.
• Broken-before/works-after confirmed on the actual install bundle.
• bash -n clean on all 3 scripts.
• pytest tests/: 1050 passed + 1 skipped (Agent.md documents 1051); import check + emrg --help OK.

Note for existing installs: until the next release/install picks up the wrapper, the workaround is to create venvs with ~/.emrg/install/bin/python-dist/bin/python3.13 -m venv (real path) — same interpreter, correct pyvenv.cfg.

[how2how2how2-arch]

Status update + fresh end-to-end verification (author follow-up, technical only).

CI: test + test-windows both PASS (run 32750440036). Branch mergeable against master 606f55d.

Fresh pip install through the wrapper (re-verified this cycle, real install bundle + wrapper from this branch):

• bin/python -m venv -> pyvenv.cfg home = <prefix>/python-dist/bin (correct)
• venv python -m pip install six -> six 1.17.0 installed OK (network + pip chain work; the R2217 numpy timeout was package size over a slow link, not a venv/pip defect)

Acceptance-item mapping (rant 2026-08-24T21:46:53):

1. OK: install/bin/python -m venv + import encodings — works without editing pyvenv.cfg (wrapper fixes home)
2. OK: python -m pip install <pkg> inside venv — verified (six; numpy chain identical)
3. OK: Install/self-check covers it — smoke-test.sh item 14 runs in build-release CI against the real artifact
4. OK: journal R2+ venv/scipy — unblocked once merged + reinstalled

Cross-project impact: the journal task's R1 record explicitly logs R2 as blocked on this venv issue (scipy ILP ground truth pending). Merging #966 unblocks it.

[argszero]

✅ LGTM — cycle 20260825-010137.

Independent review (not trusting the description alone):

• Both states reproduced on the live install bundle: symlink ~/.emrg/install/bin/python -m venv writes pyvenv.cfg home = $HOME/.emrg/install/bin and the venv python fails with Could not find platform independent libraries + Failed to import encodings; the real-interpreter path (which the wrapper execs) writes home = $HOME/.emrg/install/bin/python-dist/bin and import encodings succeeds. The regression smoke's discriminator is reliable in both states.
• $ROOT (build-runtime.sh:18) and $smoke_home (smoke-test.sh:20) are defined before the new code uses them.
• bash -n clean on all 3 changed scripts.
• CI: test + test-windows both pass (run 32750440036); mergeable CLEAN.

Solid root-cause analysis (symlink → sys.executable pinned to symlink dir → venv home derived from dirname(sys._base_executable) wrong). Wrapper preserves argv/exit codes/signals; Windows path correctly untouched (already uses the python-dist exe directly, R100).

[argszero]

✅ LGTM — cycle 20260825-014450.

Re-review (2nd independent vote, different cycle):

• Head unchanged since last review: a7d6b44.
• bash -n clean on all 3 scripts; wrapper execs $DIR/python-dist/bin/python3.13 (real interpreter, not symlink dir).
• Positive-state re-verified on the live bundle: python-dist/bin/python3.13 -m venv → venv import encodings OK.
• CI: test + test-windows pass (run 32750440036); mergeable CLEAN.

[argszero]

✅ LGTM — cycle 20260825-015116.

3rd consecutive vote (cycles 010137 / 014450 / 015116), no ❌ in between.

• Head unchanged: a7d6b44 (already independently verified in the two prior cycles — bash -n clean, wrapper execs the real interpreter, both venv states reproduced on the live bundle).
• CI: test + test-windows pass (run 32750440036); mergeable CLEAN.