fix: make Git-submodule takeover failure-atomic

[ORESoftware]

Context

PR #96 merged the requested Git-submodule interoperability surface:

• opt-in zed install --git-submodules[=true|false];
• ZED_PKG_GIT_SUBMODULES and matching .cli-flags.toml metadata;
• recursive, explicit-checkout submodule synchronization before ordinary Zed resolution;
• zed overtake --git-submodules for importing committed Zed-package submodules into workspace/dependency authority; and
• additive, frozen-verifiable [[git-submodule]] provenance in .zpkg.lock.

A post-merge transaction audit found one narrow migration edge: overtake committed the candidate .zpkg.toml before invoking the ordinary installer. A resolution or materialization failure could therefore leave a half-adopted root manifest even though the installer correctly rolled back its own lock and materialized tree.

Hardening in this PR

• snapshot and parse the same exact prior root-manifest bytes;
• verify the manifest has not changed before applying takeover intent;
• restore the exact prior bytes when installation fails before commit;
• remove a newly generated root manifest when none existed before takeover;
• refuse rollback if another writer changed the candidate manifest;
• reacquire the global install lock before rollback recovery;
• distinguish additive Git-lock finalization failures, which occur after the ordinary install transaction commits, and retain the adopted manifest so disk intent stays aligned with installed state;
• add focused unit coverage plus a real Git-submodule fixture whose transitive dependency cannot resolve; and
• document the failure and reconciliation contract.

Exact-head validation

All eight pull-request workflows pass on commit 8383d8bf:

• core CI: all nine jobs, including Ubuntu/macOS nextest and doctests, all-target Clippy, Docker install boundaries, shell/help contracts, durable-manifest recovery, and Rust/Node host-plus-OCI consumer roundtrips;
• Nix interoperability on Ubuntu and macOS;
• copy-mode OCI contract;
• polyglot contract;
• development-shell contracts;
• repository hardening;
• agents policy; and
• formal review procedure.

This supersedes closed draft #98, whose history was compacted from connector-generated per-file commits into this single intentional commit without changing the four-file product tree.

Follow-up to #96 and DEN-1612.

[linear-code]

DEN-1612