fix(project): only commit files that were actually modified

[robingenz]

Problem

AndroidManifest.xml and project.pbxproj are opened into the VFS whenever the
corresponding platform directory exists, regardless of what the config asks for.
VFS.commitAll() then wrote back every open file with no modification check —
VFSRef.modified / isModified() existed but were never read anywhere in the repo.

Running a project.json-only config against a project with ios/ and android/
therefore:

• reformatted AndroidManifest.xml (one-time normalization churn: attributes collapsed
  onto one line, indentation rewritten),
• rewrote project.pbxproj byte-identically but bumped its mtime on every run,
• and listed both as updated in the CLI output.

Fix

Filtering commitAll() on isModified() alone would have been a much worse bug: only
XmlFile (and a few IosProject plist writes) called vfs.set(). PlistFile,
JsonFile, PropertiesFile, StringsFile, XCConfigFile, GradleFile and the pbxproj
all mutate their in-memory document in place and never flagged the ref — filtering first
would have silently stopped committing gradle/properties/strings/xcconfig edits.

So, in order:

1. Every file wrapper now flags its VFS ref on mutation. Added VFSRef.markModified()
   / VFS.markModified(filename) and called it from every mutating path:
   • PlistFile.setDocument/setFromXml/set/merge (update goes through setDocument)
   • JsonFile.set/merge
   • PropertiesFile.updateProperties
   • StringsFile.set
   • XCConfigFile.set
   • GradleFile — all three this.source = … sinks now go through a private setSource()
   • XmlFile.mergeFragment — the one XmlFile mutator that was missing the flag
   • IosProject — a private markPbxModified() on every method that writes build
     settings or pbxproj state (setBundleId, setProductName, setBuild,
     incrementBuild, setVersion, setBuildProperty, addFramework, addFile)
   • AndroidProject.setAppName poked the manifest DOM directly, bypassing XmlFile;
     it now goes through XmlFile.setAttrs
2. Then VFS.commitAll(), VFS.diffAll() and checkModifiedFiles() in the CLI filter
   on the new VFS.modifiedFiles(), so untouched files are neither listed as updated
   nor rewritten.

Verified locally

• packages/project: 126 tests / 20 files passed (Java 21 present, gradle tests real)
• packages/configure: 71 tests / 23 files passed
• New tests:
  • run.test.ts — the Project config files touched/updated even if not in yaml #110 repro: a project-only config against the ios-and-android
    fixture leaves AndroidManifest.xml and project.pbxproj byte-identical and
    un-touched (mtime), and vfs.modifiedFiles() contains only the two project files.
    Confirmed it fails without the fix, with exactly the reported reformatting diff.
  • A "writes to disk on commit" guard for each file type — json, plist, strings,
    xcconfig, gradle, pbxproj build settings (properties and xml already had one).
    Confirmed all seven fail when markModified() is stubbed out, i.e. they really do
    guard against the trap above.
  • vfs.test.ts — commitAll() commits only modified refs.
  • project.android.test.ts — setAppName writes the manifest when there is no
    android:label (the direct-DOM path). Confirmed it fails if that path is reverted.

Closes #110

🤖 Generated with Claude Code

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Project	Deployment	Actions	Updated (UTC)
trapeze	Ready	Preview	Aug 15, 2026 8:31am

[Copilot]

Pull request overview

This PR updates Trapeze’s VFS and file wrappers so that only files actually mutated during a run are considered “modified” and therefore are the only ones diffed, listed as updated, and written back to disk. This directly addresses the churn/touching of AndroidManifest.xml and project.pbxproj reported in #110 when a config doesn’t target those platforms.

Changes:

• Add explicit “modified” tracking in the VFS (markModified(), modifiedFiles()) and filter commitAll() / diffAll() to only act on modified refs.
• Ensure every mutating code path in file wrappers and platform projects flags its VFS entry as modified (including in-place mutations like pbxproj and Gradle source updates).
• Add/extend tests to prevent regressions (commit/diff filtering, pbxproj/manifest writes, and “untouched files remain untouched” integration coverage in run).

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
packages/project/src/vfs.ts	Adds markModified()/modifiedFiles() and filters commit/diff operations to modified refs only.
packages/project/src/xml.ts	Ensures mergeFragment() marks the XML file as modified so it’s committed when changed.
packages/project/src/plist.ts	Flags plist VFS refs on in-place document mutations so commits aren’t skipped.
packages/project/src/json.ts	Flags JSON VFS refs on in-place document mutations so commits aren’t skipped.
packages/project/src/properties.ts	Flags properties VFS refs when updating merged properties.
packages/project/src/strings.ts	Flags strings VFS refs when values are set in-place.
packages/project/src/xcconfig.ts	Flags xcconfig VFS refs when content is updated.
packages/project/src/android/gradle-file.ts	Funnels Gradle source mutations through setSource() to consistently mark modified.
packages/project/src/android/project.ts	Routes manifest label updates through XmlFile.setAttrs() to ensure modifications are tracked/committed.
packages/project/src/ios/project.ts	Tracks the pbxproj VFS ref and marks it modified on in-place pbx project mutations.
packages/project/test/vfs.test.ts	Adds unit test asserting commitAll() only commits modified files.
packages/project/test/project.android.test.ts	Adds test ensuring manifest label is written when android:label was missing.
packages/configure/src/tasks/run.ts	Switches CLI “updated” listing to only show modified files.
packages/configure/test/tasks/run.test.ts	Adds integration repro test to ensure untouched platform files remain byte-identical and not re-touched.
packages/configure/test/ops/android.json.test.ts	Adds guard test ensuring JSON changes are actually written on commit.
packages/configure/test/ops/android.gradle.test.ts	Adds guard test ensuring Gradle changes are actually written on commit.
packages/configure/test/ops/ios.plist.test.ts	Adds guard test ensuring plist changes are actually written on commit.
packages/configure/test/ops/ios.strings.test.ts	Adds guard test ensuring strings changes are actually written on commit.
packages/configure/test/ops/ios.xcconfig.test.ts	Adds guard test ensuring xcconfig changes are actually written on commit.
packages/configure/test/ops/ios.buildVersion.test.ts	Adds guard test ensuring pbxproj build setting changes are actually written on commit.

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