fix(workspace): materialize and classify executables correctly (backport of #338, #339)

[bobtista]

Summary

Backports #338 and #339 into release/alpha-4.

• fix(workspace): materialize executables atomically and repair stale modes #338 — materialize executables atomically and repair stale execute modes.
• fix(content): classify executables by magic bytes instead of the extensionless heuristic #339 — classify executables by magic bytes instead of the extensionless
  heuristic.

Both bear on whether a prepared workspace produces a launchable entry point,
which is the A profile can be created and launched box still open for both
platforms in #307.

Why these two

They are the same class of user-facing workspace fix as #346 and #350, both
already backported. The remaining development commits are deliberately left
out:

• feat(platform): make paths, manifests, and Unix workspaces platform-aware #328, feat(macos): add native host, installation detection, and CI #329, fix(macos): register the platform services the merged state requires #331 — Alpha 5 platform work, excluded by the split described in chore: alpha 4 release #335.
• feat(launching): launch the native BGFX client against retail archives #332 — native BGFX client launch, a feature rather than a fix.
• fix(tests): pass the absolute path to the executable classifier #345 — only touches NativeClientManifestLaunchTests.cs, a file created by
  feat(launching): launch the native BGFX client against retail archives #332, so it is a no-op on this branch.

Backport notes

#339 cherry-picked clean. #338 required one adaptation, worth recording because
a clean textual merge hides it:

On development, #338 merged before #348, the forward-port of #346. This
branch already carries #346, so the cherry-pick applies #338 after it —
reversing the integration order. #348 had amended #338's own tests to coexist
with the workspace-root change, rewriting
Path.Combine(_tempPath, "workspace") to Path.Combine(_tempPath, workspaceId)
so the cached workspace path matches the root-derived path and the recreate
branch does not fire.

Without that adaptation the cherry-pick still compiles and reports no conflict in
WorkspaceManager.cs, but
PrepareWorkspaceAsync_WhenEntryPointBricked_RepairsAndReusesWorkspace fails.
The same two-line adaptation #348 made is folded into the #338 commit here, so
both commits are individually green.

The one genuine conflict was in WorkspaceManagerReuseTests.cs, where #346's
WhenStorageRootChanges test and #338's two new tests landed adjacently. All
three are kept; #338's change to that file is purely additive.

Testing

• dotnet test GenHub/GenHub.Tests/GenHub.Tests.Core/GenHub.Tests.Core.csproj -c Release
  • At #338: 1,478 passed, 0 failed
  • At #339 (tip): 1,510 passed, 0 failed
• dotnet build GenHub/GenHub.Linux/GenHub.Linux.csproj -c Release — passed
• Formatting verification and git diff --check — passed

Risks and rollback

• release/alpha-4 still lacks the blank-root guard fix(workspace): fall back from protected adjacent storage (forward-port of #346) #348 added on top of fix(workspace): fall back from protected adjacent storage #346 in
  WorkspaceManager. No test exercises it and nothing here depends on it, but
  this branch carries a slightly older variant of that fix than development.
• Reverting either commit restores the previous executable materialization and
  classification behavior.

Outstanding

Packaged Windows and Linux validation per #307 still applies; these commits
change workspace materialization, so the profile can be created and launched
checks should be re-run against a build containing them.

Backport of #338 and #339

Greptile Summary

This backport makes Unix executable materialization atomic, repairs stale executable modes when reusing workspaces, and centralizes executable classification around file extensions and magic bytes.

• Adds private-copy executable swaps to protect hard-linked CAS content.
• Validates and repairs cached workspace entry points before reuse.
• Distinguishes native binaries, scripts, libraries, and legacy launch candidates across manifest-generation paths.
• Adds focused tests for atomic replacement, CAS isolation, path containment, workspace reuse, and executable magic formats.

Confidence Score: 5/5

The PR appears safe to merge, with no concrete changed-code defect identified.

The executable swap preserves CAS isolation, workspace reuse repairs only contained entry points, unsafe or missing paths fall back to recreation, and changed classifier callers consistently select content-aware or metadata-only classification according to the available file state.

Important Files Changed

Filename	Overview
GenHub/GenHub.Core/Utilities/ExecutableFileClassifier.cs	Adds bounded header sniffing for PE, ELF, and Mach-O files while retaining explicit name-only APIs for metadata contexts.
GenHub/GenHub/Features/Workspace/ExecutableFileSwap.cs	Introduces unique temporary copies and atomic replacement so execute-mode changes cannot mutate shared hard-link targets.
GenHub/GenHub/Features/Workspace/WorkspaceValidator.cs	Adds contained-path entry-point repair with parent-symlink checks and structured failures that trigger recreation.
GenHub/GenHub/Features/Workspace/WorkspaceManager.cs	Checks and repairs the entry point before returning a reused workspace, recreating the workspace when repair is unsafe or impossible.
GenHub/GenHub/Features/Workspace/Strategies/WorkspaceStrategyBase.cs	Delegates executable materialization to the shared atomic swap helper.
GenHub/GenHub.Core/Models/Manifest/ManifestVariantResolver.cs	Explicitly uses name-only legacy launch classification because manifest resolution operates on metadata rather than acquired files.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[Prepare workspace] --> B{Reusable cached workspace?}
    B -- No --> C[Materialize files]
    C --> D[Copy executable to unique temporary path]
    D --> E[Apply Unix execute mode]
    E --> F[Atomically replace workspace file]
    B -- Yes --> G[Resolve contained entry point]
    G --> H{Exists and executable?}
    H -- Yes --> I[Reuse workspace]
    H -- Missing or unsafe --> C
    H -- Mode missing --> J[Create executable private copy]
    J --> I

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Context used (3)

• Knowledge Base — Workspace Assembly
• Knowledge Base — Content Manifest System
• Knowledge Base — Content Acquisition Pipeline

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