Enhance editor features, improve performance, and fix bugs

[Szowesgad]

This pull request introduces several significant improvements and new features to the Pensieve macOS markdown editor, focused on agent prompt dispatching, transcription integration, build and clean process enhancements, and package configuration. The most notable changes are the addition of agent prompt dispatching infrastructure, integration of a transcription panel with new document and agent actions, and improvements to the build system for robustness and CI support.

Agent Prompt Dispatching & Transcription Integration:

• Added the AgentPromptDispatcher infrastructure, enabling dispatching of prompts to an external agent process and parsing its output, along with a new AgentPromptLaunching protocol and a concrete implementation (VibecraftedAgentPromptLauncher). This allows the app to send prompts (such as transcriptions) to an external tool and receive structured feedback.
• Integrated a new transcription panel (TranscriptionTaflaPanelController) into AppController, with methods to show/hide/toggle the panel and send transcriptions either to the active editor or dispatch them to the agent. The transcription dispatch process is now asynchronous and updates status in the UI. [1] [2] [3]

Document and Window Management:

• Refactored document and window management in AppController, adding methods for opening/closing files and windows, clearing open files, and improved logic for switching between documents and tabs. This provides a more robust and flexible user experience, especially when handling multiple documents. [1] [2] [3]

Build System & CI Improvements:

• Added a new install-app target to the Makefile for atomically installing the signed .app bundle to /Applications, including safe process quitting and relaunching. Improved the clean target to avoid race conditions with live indexers by atomically renaming before deletion.
• Updated the lint and format targets to exclude generated files from formatting checks, ensuring faster and more reliable linting.
• Introduced a GitHub Actions CI workflow (ci.yml) that runs tests on pushes and pull requests to the main branch, improving code quality assurance.

Swift Package Configuration:

• Enhanced Package.swift to support linking with the external qube_ffi library, including dynamic linker flags and a new systemLibrary target for qube_ffiFFI. This sets up the infrastructure for integrating native code via FFI. [1] [2] [3]

Other Changes:

• Removed the .claude/settings.local.json permissions file.
• Minor bug fixes and code cleanups, such as correcting untitled document title generation and simplifying tab navigation to use native macOS window tab actions. [1] [2]

References:

• Agent prompt dispatching and integration: [1] [2] [3] [4]
• Document/window management: [1] [2] [3]
• Build system and CI: [1] [2] [3]
• Swift package configuration: [1] [2] [3]
• Miscellaneous: [1] [2] [3]

[gemini-code-assist]

Code Review

This pull request introduces several significant features to the Pensieve markdown editor, including a voice transcription service with a floating 'Tafla' panel, an autocomplete controller powered by a native Rust FFI bridge, multi-window document routing, document recovery for untitled drafts, and HTML/PDF export capabilities. It also optimizes workspace scanning by honoring .gitignore rules and moves database operations off the main thread. The code review feedback identifies critical issues that need to be addressed, such as hardcoded user home directory paths, potential data races in IndexDatabase requiring synchronization, main-thread blocking during PDF export, a dictionary memory leak in DocumentWindowRegistry, incorrect CRLF line ending handling in .gitignore parsing, and threading issues in AutocompleteController.

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[gemini-code-assist]

The executable path is hardcoded to a specific user's home directory (/Users/maciejgad). This will fail on any other machine. Use NSHomeDirectory() to dynamically construct the path relative to the current user's home directory.

  static var executablePath: String {
    let home = NSHomeDirectory()
    return "\(home)/.local/share/vibecrafted/tools/vibecrafted-current/scripts/vibecrafted"
  }

[gemini-code-assist]

The workspace root is hardcoded to /Users/maciejgad/.... This should be constructed dynamically using the current user's home directory to ensure portability across different development environments.

Suggested change

	agentWorkspaceRoot: URL = URL(
	fileURLWithPath: "/Users/maciejgad/vc-workspace/vetcoders/pensieve"),
	agentWorkspaceRoot: URL = FileManager.default.homeDirectoryForCurrentUser
	.appendingPathComponent("vc-workspace/vetcoders/pensieve"),

[gemini-code-assist]

Since IndexDatabase is accessed concurrently from multiple background tasks and the main thread, the mutable properties databasePool, databaseURL, and openTask are subject to data races. Introduce an NSRecursiveLock to synchronize access to these properties.

Suggested change

	/// Coalesces concurrent off-main opens: the first `ensureOpenInBackground` that finds no pool
	/// starts the migration on a detached executor and parks this task; later callers await the SAME
	/// task instead of racing a second `DatabasePool`/migration. Cleared once the open resolves.
	private var openTask: Task<DatabasePool, Error>?
	/// Coalesces concurrent off-main opens: the first `ensureOpenInBackground` that finds no pool
	/// starts the migration on a detached executor and parks this task; later callers await the SAME
	/// task instead of racing a second `DatabasePool`/migration. Cleared once the open resolves.
	private var openTask: Task<DatabasePool, Error>?
	private let lock = NSRecursiveLock()

[gemini-code-assist]

Synchronize the synchronous open(into:) method using the recursive lock to prevent data races when called concurrently with background open operations.

Suggested change

	func open(into appState: AppState? = nil) {
	do {
	let url: URL
	if let configuredDatabaseURL {
	url = configuredDatabaseURL
	} else {
	let directory = try applicationSupportDirectory()
	url = directory.appendingPathComponent("index.db", isDirectory: false)
	}
	let url = try resolveDatabaseURL()
	let pool = try Self.makeDatabasePool(at: url)
	databasePool = pool
	databaseURL = url
	} catch {
	reportOpenFailure(error, appState: appState)
	}
	}
	func open(into appState: AppState? = nil) {
	lock.lock()
	defer { lock.unlock() }
	do {
	let url = try resolveDatabaseURL()
	let pool = try Self.makeDatabasePool(at: url)
	databasePool = pool
	databaseURL = url
	} catch {
	reportOpenFailure(error, appState: appState)
	}
	}

[gemini-code-assist]

Implement thread-safe synchronization in ensureOpenInBackground using the recursive lock to safely manage concurrent database pool initialization and avoid data races on databasePool and openTask.

  private func ensureOpenInBackground(into appState: AppState?) async -> DatabasePool? {
    lock.lock()
    if let databasePool {
      lock.unlock()
      return databasePool
    }
    if let openTask {
      lock.unlock()
      return try? await openTask.value
    }

    let url: URL
    do {
      url = try resolveDatabaseURL()
    } catch {
      lock.unlock()
      reportOpenFailure(error, appState: appState)
      return nil
    }

    let task = Task<DatabasePool, Error> {
      try await Task.detached(priority: .userInitiated) {
        try Self.makeDatabasePool(at: url)
      }.value
    }
    openTask = task
    lock.unlock()

    do {
      let pool = try await task.value
      lock.lock()
      databasePool = pool
      databaseURL = url
      openTask = nil
      lock.unlock()
      return pool
    } catch {
      lock.lock()
      openTask = nil
      lock.unlock()
      reportOpenFailure(error, appState: appState)
      return nil
    }
  }

[gemini-code-assist]

Writing the PDF data to disk is currently performed synchronously on the main thread (since PDFExportJob is @MainActor). This can block the UI and cause beachballing for larger documents. Perform the write operation asynchronously on a background queue.

      case .success(let data):
        let url = self.outputURL
        DispatchQueue.global(qos: .userInitiated).async {
          do {
            try data.write(to: url, options: .atomic)
            DispatchQueue.main.async {
              self.finish(.success(()))
            }
          } catch {
            DispatchQueue.main.async {
              self.finish(.failure(error))
            }
          }
        }

[gemini-code-assist]

The windowsByDocumentID dictionary holds WeakWindow wrappers. When a window is closed, the weak reference inside WeakWindow becomes nil, but the key (the document URL) remains in the dictionary forever. Filter windowsByDocumentID during the sweep to prevent a memory leak of dictionary entries.

Suggested change

	private func purgeClosedLauncherWindows() {
	launcherWindows = launcherWindows.filter { $0.value.window != nil }
	contentWindows = contentWindows.filter { $0.value.window != nil }
	if let preferredLauncherID, launcherWindows[preferredLauncherID]?.window == nil {
	self.preferredLauncherID = nil
	}
	}
	private func purgeClosedLauncherWindows() {
	launcherWindows = launcherWindows.filter { $0.value.window != nil }
	contentWindows = contentWindows.filter { $0.value.window != nil }
	windowsByDocumentID = windowsByDocumentID.filter { $0.value.window != nil }
	if let preferredLauncherID, launcherWindows[preferredLauncherID]?.window == nil {
	self.preferredLauncherID = nil
	}
	}

[gemini-code-assist]

Trimming only whitespaces (rawLine.trimmingCharacters(in: .whitespaces)) does not remove carriage returns (\r) from files with CRLF line endings (common on Windows or when git autocrlf is enabled). This causes pattern matching to fail. Trim both whitespaces and newlines to handle CRLF line endings correctly.

Suggested change

	init?(line rawLine: String, baseRelativePath: String) {
	var line = rawLine.trimmingCharacters(in: .whitespaces)
	init?(line rawLine: String, baseRelativePath: String) {
	var line = rawLine.trimmingCharacters(in: .whitespacesAndNewlines)

[gemini-code-assist]

AutocompleteController is an ObservableObject whose @Published properties are updated from asynchronous tasks. To prevent threading issues and SwiftUI runtime warnings, the entire class should be marked with @MainActor.

Suggested change

	final class AutocompleteController: ObservableObject, @unchecked Sendable {
	@MainActor
	final class AutocompleteController: ObservableObject {

[Copilot]

Pull request overview

This PR significantly expands Pensieve’s editor/runtime capabilities by adding transcription (“Tafla”) tooling, agent prompt dispatch infrastructure, multi-window/tab routing, richer markdown rendering (wikilinks + math), and build/CI improvements (FFI linking + signed app installation + workflow).

Changes:

• Added transcription accumulation/service + a floating Tafla panel, with routing to editor insertion or agent dispatch.
• Introduced editor enhancements: inline highlight syntax, markdown autoconversion while typing, AI autocomplete plumbing, and scroll/format-bar UX changes.
• Improved preview pipeline and markdown rendering: incremental preview updates, base URL handling, wikilinks, and math nodes + bootstrap scripts.
• Added window/document routing infrastructure (window registry + per-window model/state split) and build/CI updates (FFI embedding/linking, Makefile targets, GitHub Actions).

Reviewed changes

Copilot reviewed 66 out of 69 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
VERSION	Bumps app version to 0.2.7.
SECURITY.md	Adds security policy and vulnerability reporting guidance.
scripts/build-release.sh	Embeds and re-signs libqube_ffi.dylib inside the app bundle for hardened runtime.
Pensieve/Tests/PensieveTests/WorkspaceSubstrateTests.swift	Adds assertions around file protection when writing workspace cache/metadata artifacts.
Pensieve/Tests/PensieveTests/TranscriptionTaflaPanelTests.swift	Adds UI configuration tests for the Tafla floating panel.
Pensieve/Tests/PensieveTests/TranscriptionAccumulationTests.swift	Adds extensive tests for transcription buffering/formatting and routing to editor/agent.
Pensieve/Tests/PensieveTests/SyntaxHighlighterTests.swift	Adds coverage for inline ==highlight== background rendering.
Pensieve/Tests/PensieveTests/QubeFfiBridgeSmokeTests.swift	Adds a compile/surface smoke test for the Vista engine bridge.
Pensieve/Tests/PensieveTests/PreviewPipelineTests.swift	Extends preview document tests (sourceURL/refreshToken, math bootstrap, body/style extraction).
Pensieve/Tests/PensieveTests/MarkdownWikilinksTests.swift	Adds extraction/rendering tests for [[wikilinks]].
Pensieve/Tests/PensieveTests/MarkdownFormatterTests.swift	Adds typing autoconversion + typewriter-scroll tests; updates representable init parameters.
Pensieve/Tests/PensieveTests/MarkdownBlockMapperTests.swift	Adds tests for block-index mapping used for scroll sync.
Pensieve/Tests/PensieveTests/IndexDatabaseV2StatsTests.swift	Improves unwrap diagnostics and aligns bookmark store setup with throwing APIs.
Pensieve/Tests/PensieveTests/IndexDatabaseV2FtsTriggerTests.swift	Switches ad-hoc indexing tests to await background indexing completion.
Pensieve/Tests/PensieveTests/IndexDatabaseExternalContentFtsTests.swift	Updates docs + awaits background indexing for deterministic assertions.
Pensieve/Tests/PensieveTests/IndexDatabaseBacklinksTests.swift	Adds backlink resolution tests for wikilinks and workspace scoping.
Pensieve/Tests/PensieveTests/HTMLEmitterTests.swift	Adds HTML emission tests for inline/display math and coexistence with wikilinks.
Pensieve/Tests/PensieveTests/DocumentExportTests.swift	Adds export HTML rendering and file-name defaulting tests.
Pensieve/Tests/PensieveTests/AutocompleteControllerTests.swift	Adds debounce/cancellation and surface integration tests for autocomplete.
Pensieve/Sources/qube_ffiFFI/module.modulemap	Adds modulemap for the system library target exposing the FFI header.
Pensieve/Sources/Pensieve/Workspace/WorkspaceMetadataStore.swift	Writes metadata with file-protection options (with fallback).
Pensieve/Sources/Pensieve/Workspace/WorkspaceCacheStore.swift	Writes cache artifacts with file-protection options (with fallback).
Pensieve/Sources/Pensieve/Transcription/TranscriptionTaflaPanel.swift	Adds a floating non-activating SwiftUI/AppKit transcription panel.
Pensieve/Sources/Pensieve/Transcription/TranscriptionService.swift	Implements transcription accumulation, cadence commits, formatting, and dispatch status.
Pensieve/Sources/Pensieve/Storage/RecoveryStore.swift	Adds crash-recovery draft persistence/loading/deletion.
Pensieve/Sources/Pensieve/Sidebar/SidebarView.swift	Adds “Clear Open Files” and ad-hoc close action; routes open to new window handler.
Pensieve/Sources/Pensieve/Search/WorkspaceSearchResult.swift	Adds a backlink result model for backlink UI/workflows.
Pensieve/Sources/Pensieve/Resources/markdown.css	Styles wikilink anchors in the default theme.
Pensieve/Sources/Pensieve/Resources/gfm.css	Styles wikilink anchors in the GFM theme.
Pensieve/Sources/Pensieve/Preview/PreviewWebView.swift	Adds incremental update path + math styling/bootstrap + accessibility identifier.
Pensieve/Sources/Pensieve/Preview/PreviewPipeline.swift	Extends PreviewDocument with body/style/maths/identity fields + base tag insertion.
Pensieve/Sources/Pensieve/Markdown/MarkdownWikilinks.swift	Implements wikilink parsing, rendering, and slugging.
Pensieve/Sources/Pensieve/Markdown/MarkdownMath.swift	Adds math delimiter parsing and math-node rendering with escaped TeX.
Pensieve/Sources/Pensieve/Markdown/HTMLEmitter.swift	Routes text rendering through math/wikilink renderers; avoids nesting in markdown links.
Pensieve/Sources/Pensieve/Editor/SyntaxHighlighter.swift	Adds inline ==highlight== regex and attributes.
Pensieve/Sources/Pensieve/Editor/MarkdownTextView.swift	Adds autocomplete ghost rendering + in-window draggable formatting bar + insert helper.
Pensieve/Sources/Pensieve/Editor/MarkdownFormatter.swift	Adds typing autoconversion logic (lists/quotes + inline highlight closure).
Pensieve/Sources/Pensieve/Editor/MarkdownBlockMapper.swift	Adds block start/index mapping for scroll syncing.
Pensieve/Sources/Pensieve/Editor/FindBar.swift	Adds a disclosure toggle to show/hide Replace inline.
Pensieve/Sources/Pensieve/Editor/EditorView.swift	Threads new editor parameters; pins scroll across SwiftUI updates; adds autocomplete wiring.
Pensieve/Sources/Pensieve/Editor/AutocompleteController.swift	Adds debounce/cancellation-based autocomplete controller + mock engine.
Pensieve/Sources/Pensieve/App/WorkspaceStore.swift	Extracts workspace state into a shared store with cached lookups + sort persistence.
Pensieve/Sources/Pensieve/App/PensieveApp.swift	Migrates to per-document WindowGroup, per-window AppState/controller, and startup presentation.
Pensieve/Sources/Pensieve/App/LaunchIntentCoordinator.swift	Adds startup decision callback and improved URL routing for multi-window behavior.
Pensieve/Sources/Pensieve/App/EditorToolbelt.swift	Makes toolbar work for any editable buffer; adds Tafla toggle + Share button.
Pensieve/Sources/Pensieve/App/DocumentWindowRegistry.swift	Adds window/tab registry to merge/activate windows and close empty launcher windows.
Pensieve/Sources/Pensieve/App/DocumentWindowModel.swift	Adds per-window persisted preferences (preview reload, table tidy, AI autocomplete).
Pensieve/Sources/Pensieve/App/DocumentSharing.swift	Adds Share-sheet routing for file-backed or unsaved buffers.
Pensieve/Sources/Pensieve/App/DocumentSession.swift	Adds recovery ID support for untitled buffers and restoration API.
Pensieve/Sources/Pensieve/App/DocumentExport.swift	Adds HTML/PDF export flows and filename sanitization.
Pensieve/Sources/Pensieve/App/ContentView.swift	Removes custom tab strip; uses toolbar toolbelt and relies on native window tabs.
Pensieve/Sources/Pensieve/App/Commands.swift	Refactors commands to focused objects; adds share/export, Tafla toggle, AI autocomplete toggle, tab bar toggle.
Pensieve/Sources/Pensieve/App/AppState.swift	Refactors into WorkspaceStore + DocumentWindowModel bridge and adds DocumentRef: Codable.
Pensieve/Sources/Pensieve/App/AppController.swift	Adds transcription + agent dispatch integration; multi-window open routing; open-files management; background DB warmup.
Pensieve/Sources/Pensieve/App/AgentPromptDispatcher.swift	Adds agent dispatch metadata parsing + launcher protocol + Process-based launcher implementation.
Pensieve/scripts/build-ffi.sh	Adds helper script to rebuild/sync UniFFI Swift bridge and the dylib into the repo.
Pensieve/Package.swift	Adds system library target and linker flags/rpath for qube_ffi dylib integration.
Makefile	Adds install-app target, improves clean robustness, excludes generated file from formatting/lint.
docs/index.html	Adds a static project landing page for docs hosting.
docs/.nojekyll	Disables Jekyll processing for docs hosting.
.gitignore	Updates ignore rules (logs, markdown governance allowlist, tmp/dist/docs exclusions).
.github/workflows/ci.yml	Adds GitHub Actions workflow running make test on macOS.
.claude/settings.local.json	Removes local Claude permissions file from the repo.

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