[#2988] Removed unmodified template-owned paths the install no longer ships.

[AlexSkrypnyk]

Closes #2988

Summary

Issue #2988 investigated why downstream projects were removing installer-selected tools by hand instead of through the installer, after three sites each removed Jest a different way. The cause is not specific to tools: FileManager::copyFiles() overlays the staged template onto the destination without a delete pass, so nothing the template stops shipping is ever removed from an existing project. References disappear while the files stay, and for tools that leftover file is what Tools::discover() uses to detect the tool, so an incomplete removal silently reverts on the next update.

This PR removes template-owned paths that the install no longer ships, in one place, for every handler - but only where the project has not touched the file.

The rule

A path is removed only when all of the following hold:

1. Either version of the template shipped it, or the last install wrote it.
2. This install's staged copy no longer holds it.
3. The project's copy still hashes to what the template put there.
4. The destination is already a Vortex project.

Anything that cannot be verified is kept. No recorded hash means no removal; a hash mismatch means the project edited the file and owns it.

Condition 2 covers both ways a path stops being shipped: excluded by the current selection, and dropped by the template between releases.

Changes

• FileManager::snapshotTemplate() records the incoming template's file list before any handler processes it.
• FileManager::snapshotPreviousTemplate() records the file hashes of the version the project currently runs, read from the README badge and downloaded from the same repository. Without it, a path the template dropped entirely is absent from the incoming download and cannot be seen at all.
• FileManager::writeManifest() records path to sha256 of the processed content each install copies into the project, as .vortex-manifest.json. This is what makes the check exact for the files the installer rewrites on the way in - their content in the project never matches the raw template file.
• FileManager::copyFiles() resolves an expected hash per candidate path, manifest first and the previous version as the fallback for projects installed before manifests existed, and removes only what still matches. Directories left empty are pruned.
• FileManager::resetStaging() empties the staging directory before the download. The download unpacks into that directory rather than replacing it, so a reused location would otherwise leave a previous run's files to be treated as shipped by this one, and copied into the project.
• Version::detectProjectRef() reads the installed reference from the README badge. It is the only place the exact version is preserved: composer.json pins the tooling package's major rather than the template's version.

No handler was modified. The fix is handler-agnostic, so it covers deselected tools, a CI provider switch leaving .circleci/ behind, dropped services, and template files removed in a later release.

removeObsoletePaths() is unchanged and still required: it covers files dropped before the version the project records, which neither snapshot can name. AhoyWorkflowTest pins that case.

Coverage

Measured against a real install, 393 shipped files: 278 are byte-identical to the raw template and 38 are rewritten by the installer. The manifest makes all of them verifiable; the previous-version fallback covers the 278 for projects that do not have a manifest yet.

Tests

FileManagerTest covers the copy layer: unmodified excluded paths removed, modified ones kept with their contents, paths with no recorded hash kept, paths dropped by the template removed, project-authored paths kept, non-Vortex destinations untouched, harness paths kept, emptied directories pruned, and the manifest written with the content that was copied.

InstallExcludedPathsTest covers the same behavior through the real install command against a pre-populated destination: unmodified removed, modified kept with contents, nothing-recorded kept, project-authored kept, harness kept, and nothing removed from a destination that is not a Vortex project.

InstallerTest covers real two-version updates in the template's own integration suite, which is the only place the cross-version case is reachable:

• testUpdateRemovesUnmodifiedFilesDroppedByTemplate - a provision script the template drops is removed, while scripts it still ships remain.
• testUpdateKeepsModifiedFilesDroppedByTemplate - the same script, edited by the project, is kept with its edit intact.
• testUpdateKeepsProjectAuthoredFiles - project files under scripts/, .docker/, .github/workflows/, .circleci/, config/, recipes/, .claude/skills/ and the project root are all kept with their contents, while the template-owned script is still removed.

Notes for review

The manifest is around 390 entries and is rewritten on every update, so each update produces a large diff in that one file. Keys are sorted so it is deterministic and readable.

It is excluded from the installer snapshot fixtures through _baseline/.ignorecontent. Included, it would appear in all 152 scenarios and churn on any template change, which would make fixture diffs unreviewable. The dedicated tests cover it instead.

removeObsoletePaths() deletes its one hardcoded path without an ownership check, unlike everything else here. It becomes redundant once projects carry manifests.

Before / After

BEFORE

  download template ──→ handlers strip excluded paths ──→ staged copy
                                                              |
                                                              v
                                            copy over destination (no delete)
                                                              |
                                                              v
                     paths excluded by selection, and paths the template
                     dropped in an earlier release, both survive forever
                                                              |
                                                              v
                                    discovery sees them -> feature re-enabled


AFTER

  manifest from last install ──→ expected hashes ──┐
  project's own version ───────→ expected hashes ──┤
                                                   |
  download template ──→ snapshot paths ────────────┤
             |                                     v
             v                          candidates = shipped - staged
  handlers strip excluded paths                    |
             |                                     v
             └──→ staged copy ──→ copy over destination
                                                   |
                                                   v
                              for each candidate still in the project:
                                 hash matches expected ──→ remove
                                 hash differs, or unknown ──→ keep

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Repository UI

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Run ID: 7100e675-ef47-4304-be53-a8b7bd8dfb9d

📥 Commits

Reviewing files that changed from the base of the PR and between dced997 and 87e545a.

📒 Files selected for processing (5)

• .vortex/installer/src/Command/InstallCommand.php
• .vortex/installer/src/Utils/FileManager.php
• .vortex/installer/src/Utils/Version.php
• .vortex/installer/tests/Functional/Command/InstallExcludedPathsTest.php
• .vortex/tests/phpunit/Functional/InstallerTest.php

---

Walkthrough

The installer now resets staging, snapshots incoming and previous templates, and removes eligible excluded paths from existing Vortex projects. Tests cover preservation rules. Documentation describes VORTEX_EXPORT_DB_FILE_STRUCTURE_TABLES.

Changes

Template pruning

Layer / File(s)	Summary
Template snapshot and destination pruning .vortex/installer/src/Command/InstallCommand.php, .vortex/installer/src/Utils/FileManager.php, .vortex/installer/src/Utils/Version.php	The installer resets staging and records incoming and previous template paths. copyFiles() removes eligible excluded paths while preserving project-authored and .vortex harness paths.
Pruning behavior validation .vortex/installer/tests/Unit/Utils/FileManagerTest.php, .vortex/installer/tests/Functional/Command/InstallExcludedPathsTest.php, .vortex/tests/phpunit/Functional/InstallerTest.php	Tests cover removal of shipped paths and preservation of never-shipped, non-Vortex, and harness paths. Update tests verify removal of a template-owned script.

Database export documentation

Layer / File(s)	Summary
Database export variable documentation .vortex/docs/content/development/variables.mdx	The documentation defines VORTEX_EXPORT_DB_FILE_STRUCTURE_TABLES, including wildcard patterns, the cache* default, and empty-value behavior.

Estimated code review effort: 3 (Moderate) | ~25 minutes

Mergeability Score: 🟠 High · up to 87e54

The installer now removes paths no longer shipped by the template, but it can also delete files that users modified locally when those files were previously template-owned. That creates a high-impact risk of project data loss, so the PR should not merge until this protection is addressed or explicitly accepted.

Sequence Diagram(s)

sequenceDiagram
  participant InstallCommand
  participant FileManager
  participant TemplateSnapshots
  participant VortexProject
  InstallCommand->>FileManager: resetStaging()
  InstallCommand->>FileManager: snapshotTemplate()
  InstallCommand->>FileManager: snapshotPreviousTemplate()
  FileManager->>TemplateSnapshots: enumerate template paths
  InstallCommand->>FileManager: copyFiles()
  FileManager->>VortexProject: remove eligible excluded paths

Loading

Possibly related PRs

• drevops/vortex#2887: Related template version detection and file synchronization changes.

Poem

A rabbit snapshots templates bright,
Then clears the staging path from sight.
Old shipped files hop away,
Authored paths remain each day.
Cache tables keep their shape—
Clean updates leave no scrap.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Out of Scope Changes check	⚠️ Warning	The environment-variable documentation change is unrelated to removing template-owned paths and falls outside issue #2988.	Move the unrelated environment-variable documentation change to a separate pull request.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The changes implement centralized removal of deselected and no-longer-shipped template paths, with protection for project-owned files and comprehensive tests [#2988].
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: removing template-owned paths that the installer no longer ships.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feature/2988-installer-opt-out

---

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[codecov]

Codecov Report

❌ Patch coverage is 84.00000% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.70%. Comparing base (852fdf1) to head (19337b7).
⚠️ Report is 5 commits behind head on main.

Files with missing lines	Patch %	Lines
.vortex/installer/src/Utils/Version.php	0.00%	8 Missing ⚠️
.vortex/installer/src/Utils/FileManager.php	93.75%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2999      +/-   ##
==========================================
- Coverage   87.11%   86.70%   -0.42%     
==========================================
  Files         101       94       -7     
  Lines        4818     4752      -66     
  Branches       47        3      -44     
==========================================
- Hits         4197     4120      -77     
- Misses        621      632      +11     

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[github-actions]

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[coderabbitai]

Actionable comments posted: 1

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Inline comments:
In @.vortex/installer/src/Utils/FileManager.php:
- Around line 148-152: Update the excluded-path handling in the destination
processing flow so existing targets are preserved rather than removed. Replace
the File::remove behavior for excluded paths with leftover reporting, while
retaining the existing handling for paths that do not exist.

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---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: ASSERTIVE

Plan: Pro Plus

Run ID: 758d3afc-319f-4ddb-980a-520c77422585

📥 Commits

Reviewing files that changed from the base of the PR and between 852fdf1 and dced997.

📒 Files selected for processing (4)

• .vortex/docs/content/development/variables.mdx
• .vortex/installer/src/Command/InstallCommand.php
• .vortex/installer/src/Utils/FileManager.php
• .vortex/installer/tests/Unit/Utils/FileManagerTest.php

[github-actions]

Code coverage (threshold: 90%)

  Classes: 100.00% (1/1)
  Methods: 100.00% (2/2)
  Lines:   98.56% (206/209)

Per-class coverage

Drupal\ys_demo\Plugin\Block\CounterBlock
  Methods: 100.00% ( 2/ 2)   Lines: 100.00% ( 10/ 10)

[AlexSkrypnyk]

Code coverage (threshold: 90%)

  Classes: 100.00% (1/1)
  Methods: 100.00% (2/2)
  Lines:   98.56% (206/209)

Per-class coverage

Drupal\ys_demo\Plugin\Block\CounterBlock
  Methods: 100.00% ( 2/ 2)   Lines: 100.00% ( 10/ 10)

[AlexSkrypnyk]

Code coverage (threshold: 90%)

  Classes: 100.00% (1/1)
  Methods: 100.00% (2/2)
  Lines:   98.56% (206/209)

Per-class coverage

Drupal\ys_demo\Plugin\Block\CounterBlock
  Methods: 100.00% ( 2/ 2)   Lines: 100.00% ( 10/ 10)