Repair runfiles trees with entries deleted out-of-band

[azad-uber-2]

If a symlink inside a runfiles tree built by a SymlinkTreeAction is
deleted from disk (e.g. by a CI disk cleaner), Bazel never restores it.
The output MANIFEST is the action's only output, so the action keeps
hitting the action cache, even across server restarts and with
--experimental_check_output_files. RunfilesTreeUpdater skips these trees,
so any spawn that reads the missing entry fails. On CI the Kotlin builder
worker fails to start on every build on the affected host:

KotlinCompile ... failed: Worker process did not return a WorkResponse:
IllegalStateException: .../build.runfiles/rules_kotlin++rules_kotlin_extensions+kotlin_build_tools_impl/file/downloaded does not exist in the runfiles!

Example (Bazel 8.8.0 shadow pipeline; 8.1.1 has the same code):
https://buildkite.com/uber/android-code-differential-bazel8/builds/6501#01a10fd3-bd05-4654-a91b-7aa51e5cbc41

Fix: before a local or worker spawn uses a runfiles tree, check once per
command that every entry exists, and resync the tree if any are missing.
The manifest-digest shortcut for --nobuild_runfile_links trees gets the
same check.

Testing on 8.1.1:

• Reproduced the failure: deleted the kotlin_build_tools_impl symlink
  from the Kotlin builder's runfiles tree in an Android output base and
  built cold with --config=buildkite on stock 8.1.1 (1657d0f). The
  build failed with the error above.
• Tested the fix: built the same damaged tree cold with the fixed binary.
  It logged "Runfiles tree ... is missing entries, recreating it." and
  the build passed.
• RunfilesTreeUpdaterTest: 2 of 3 fail without the fix; 3/3 pass with it.

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