Repository panel

Managed Repository is the managed-library panel inside Molecule Browser. It intentionally matches the Local Files panel so the same grid browsing, sort controls, Quick Look, sharing, and Finder reveal flow work there as well.

• Use Local Files for broad Spotlight-backed discovery across chemistry files already on your Mac.
• Use Managed Repository for AtomLens-managed entries you want to keep as a library.
• Managed Repository cards focus on library metadata and previews. They do not show the filesystem path for the managed copy.
• The panel refreshes from shared repository observation, so content and metadata changes can flow back into the browser automatically.
• On macOS, card context menus mirror the bottom action bar. Repository entries can be deleted from the bottom Delete... button, from a card context menu, or with Backspace after selection.
• Command-A selects all visible Managed Repository results on macOS, so multi-entry deletion and sharing can use the same selection model as Local Files.
• On iPad, each repository card has compact icon buttons for tags, sharing, and deletion. Tapping the card itself opens the item.

Example structures and reactions

The Managed Repository can be seeded with bundled example data for a first-run tour, demos, training, and App Store review. The importer adds 20 ChEBI Entity of the Month structures and 20 Rhea-derived reactions.

• The Welcome screen offers Add example structures and reactions . The option is checked by default only when the repository starts empty.
• The same importer is available later in Settings > Managed Repository with Add Example Structures and Reactions .
• Examples are stored in the same Managed Repository location as user-saved entries, using iCloud when repository sync is enabled and available.
• Duplicate checking compares molecule InChIKeys and reaction long RInChIKeys, so rerunning the importer skips examples already present in the repository.
• After import, open File > Managed Repository... and use search, Quick Look, the reactions-only filter, or direct card opening to inspect the examples.

Saving files to the repository

Use File > Save to Managed Repository... when you want AtomLens to create a managed copy of the current chemistry context.

• The repository-save flow accepts only chemistry formats that AtomLens can reopen directly in a molecule window or a reaction window.
• Visual outputs such as SVG stay in Export and Share flows. They are not offered as repository-save formats.
• On macOS, repository entries can be added through Save to Managed Repository... or from selected Local Files cards with Copy to Managed Repository .
• Move to Managed Repository... imports the selected Local Files entries and, after confirmation, moves the originals to the Trash.
• Synced content from other devices can also appear here automatically.

Sync behavior

When Sync chemical files over iCloud is enabled and the ubiquitous container is available, AtomLens resolves repository content through iCloud.de.losko.AtomLens . Managed repository metadata also follows that synced repository root.

• Remote content changes are observed and can refresh the repository browser automatically.
• Managed repository metadata such as tags and favorites now travels with the repository instead of staying purely local.
• Background-only system surfaces can still lag behind foreground UI in some real-world timing cases, but the main repository surfaces are wired into the shared observer path.

Synced metadata and Finder labels

The repository browser reads Managed Repository metadata and, while AtomLens is running on macOS, mirrors synced repository tags back into Finder labels more aggressively than the old in-app-only bridge.

• Repository tags and favorites are part of the synced metadata story now.
• Finder label changes made in the repository browser remain visible both in AtomLens and in Finder.
• Remote synced tag changes can be reflected back into Finder while AtomLens is active, which keeps cross-device label state more coherent.

When sync is off

If you turn off Sync chemical files over iCloud in AtomLens Settings, the Managed Repository remains available and stores content locally on this device.

• Local Files continues to provide broad Spotlight-backed discovery across files outside AtomLens.
• The Managed Repository panel, toolbar button, File menu item, and save workflow stay visible.
• On iPad, Browse , Save , extraction results, Files, Quick Look, and repository search continue to use the local Managed Repository.
• You can turn sync back on later from Settings to move managed content back to iCloud when available.