Regenerate native PHP mu-plugins when an existing file has stale content

[sejas]

Related issues

• Related to STU-1945
• Fixes STU-2054

How AI was used in this PR

AI assisted with the implementation, tests, and verification; all changes were reviewed and validated manually against a live native PHP site.

Proposed Changes

Sites running on the native PHP runtime never picked up updated Studio mu-plugin content. Studio writes its mu-plugins to a temp directory and reuses that directory on subsequent site starts when it looks valid — but the validity check only compared plugin filenames. When a Studio update changed a plugin's content without renaming the file (e.g. the upcoming STU-1945 change that also disables Jetpack Stats in 0-deactivate-jetpack-modules.php), existing sites kept loading the stale version forever; only newly created sites got the updated behavior.

The reuse check now also compares each plugin file's content against what the current Studio version generates, and regenerates the whole directory on any mismatch. As a bonus, partially written or corrupted plugin files now self-heal on the next site start instead of being silently reused.

No user-visible behavior change for up-to-date sites: the directory is still reused when contents match, so there is no extra churn on every start or wp-cli invocation.

Testing Instructions

• Apply this diff

diff --git a/packages/common/lib/mu-plugins.ts b/packages/common/lib/mu-plugins.ts
index 200c9277e..2cd79386e 100644
--- a/packages/common/lib/mu-plugins.ts
+++ b/packages/common/lib/mu-plugins.ts
@@ -339,6 +339,7 @@ function getStandardMuPlugins( options: MuPluginOptions ): MuPlugin[] {
 	muPlugins.push( {
 		filename: '0-deactivate-jetpack-modules.php',
 		content: `<?php
+			die('This mu-plugin got updated! 🔥');
 			// Disable Jetpack Protect so local auto-login is not blocked by 2FA.
 			// Disable Jetpack Stats so local previews and thumbnails do not bump remote site stats.
 			add_filter( 'jetpack_active_modules', 'studio_deactivate_jetpack_modules' );

• npm run start and start a native PHP site.
• Open the site and confirm the message from the diff appears, meaning the mu-plugin got updated
• On trunk the mu-plugin was only updated for new sites and not existing ones

Pre-merge Checklist

• Have you checked for TypeScript, React or other console errors?

[wpmobilebot]

📊 Performance Test Results

Comparing e55c2a3 vs trunk

app-size

Metric	trunk	e55c2a3	Diff	Change
App Size (Mac)	1352.85 MB	1352.85 MB	+0.00 MB	⚪ 0.0%

site-editor

Metric	trunk	e55c2a3	Diff	Change
load	1069 ms	1062 ms	7 ms	⚪ 0.0%

site-startup

Metric	trunk	e55c2a3	Diff	Change
siteCreation	7003 ms	6988 ms	15 ms	⚪ 0.0%
siteStartup	2359 ms	2350 ms	9 ms	⚪ 0.0%

---

Results are median values from multiple test runs.

Legend: 🟢 Improvement (faster) | 🔴 Regression (slower) | ⚪ No change (<50ms diff)

[bcotrim]

Nice catch 🙌
Tested and confirmed the behavior and the fix, LGTM 👍