refactor(self-update): use active markers instead of lifetime locks

[BlackHole1]

The previous process-lifetime version lock prevented concurrent CLI invocations on the same version from coexisting, because each process held an exclusive lock on the version lock file for its entire run.

Split the lock into two concerns: install locks guard mutation of a version directory, while per-process active markers advertise which versions are currently in use. Multiple processes can now run the same version simultaneously, and a self-update that targets a version held by another process now returns a busy outcome before clobbering its on-disk binary.

[coderabbitai]

Summary by CodeRabbit

Release Notes

• Refactor
  • Strengthened self-update system with improved detection and prevention of concurrent update attempts.
  • Enhanced version protection mechanisms during updates for better reliability.
  • Refined lock cleanup to more effectively remove stale entries and prevent update conflicts.
  • Processes attempting simultaneous updates now receive feedback about active ownership.

Walkthrough

This PR refactors the self-update version locking mechanism from a single process-lifetime lock model to a split filesystem layout with three lock types: active version markers (per-process under active/<version>/), install version locks (under install/), and legacy locks. The implementation adds install-lock reference counting to handle repeated acquisitions by the same process, stale-lock cleanup across all types, ownership discovery and liveness checks, and integration into the CLI bootstrap and core update flow. Busy outcomes now propagate from install-lock acquisition and active-owner checks in version materialization.

Possibly related PRs

• oomol-lab/oo-cli#132: Both PRs modify materializeTargetVersion and busy/owner coordination in the self-update core flow.
• oomol-lab/oo-cli#77: The main PR refactors current-version coordination via active markers and updates run-cli.ts initialization/cleanup, directly overlapping with that PR's managed install/update flow wiring.

🚥 Pre-merge checks | ✅ 4

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The pull request title follows the required format and clearly describes the main refactoring change of replacing lifetime locks with active markers.
Description check	✅ Passed	The description is directly related to the changeset, explaining the motivation and benefits of replacing process-lifetime locks with active markers and install locks.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

src/application/self-update/lock.ts (1)

627-633: ⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Handle non-directory lock paths gracefully in readDirectoryEntries.

If a lock path expected to be a directory is actually a file, readdir throws and aborts stale-cleanup/active-owner discovery instead of skipping malformed entries. This can block self-update flows.

Suggested fix

 async function readDirectoryEntries(path: string): Promise<string[]> {
     try {
         return await readdir(path);
     }
     catch (error) {
-        if (isPathMissingError(error)) {
+        if (isPathMissingError(error) || isDirectoryReadError(error)) {
             return [];
         }

         throw error;
     }
 }

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/application/self-update/lock.ts` around lines 627 - 633,
readDirectoryEntries currently treats only missing-path errors via
isPathMissingError, but if the lock path is a file (readdir throws ENOTDIR or
equivalent) it aborts cleanup; update readDirectoryEntries to also treat "not a
directory" errors as non-fatal by detecting the error code/name (e.g., ENOTDIR
or error indicating the path is not a directory) and return an empty array (skip
the malformed entry) instead of rethrowing; keep rethrowing for unexpected
errors and reference the existing readDirectoryEntries function and
isPathMissingError predicate when implementing the extra check.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Outside diff comments:
In `@src/application/self-update/lock.ts`:
- Around line 627-633: readDirectoryEntries currently treats only missing-path
errors via isPathMissingError, but if the lock path is a file (readdir throws
ENOTDIR or equivalent) it aborts cleanup; update readDirectoryEntries to also
treat "not a directory" errors as non-fatal by detecting the error code/name
(e.g., ENOTDIR or error indicating the path is not a directory) and return an
empty array (skip the malformed entry) instead of rethrowing; keep rethrowing
for unexpected errors and reference the existing readDirectoryEntries function
and isPathMissingError predicate when implementing the extra check.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: f12ea5b8-b1ad-46e4-be4b-3e28fa99aecd

📥 Commits

Reviewing files that changed from the base of the PR and between 7b1da7f and 763541b.

📒 Files selected for processing (7)

• src/application/bootstrap/run-cli.ts
• src/application/self-update/core.test.ts
• src/application/self-update/core.ts
• src/application/self-update/lock.test.ts
• src/application/self-update/lock.ts
• src/application/self-update/paths.test.ts
• src/application/self-update/paths.ts