Apps fixes

[krokicki]

A batch of fixes and refinements to the Apps feature, covering private-repo support over SSH, consistent app naming, accurate error messages, pinned/canonical GitHub URLs that fix the false "not in your library" state, and assorted UI polish.

Changes

Private repository support (SSH)

• Accept SSH GitHub URLs (git@github.com:owner/repo.git and ssh://git@github.com/owner/repo) in addition to HTTPS, in both the backend parser and the frontend.
• When an HTTPS clone fails for auth/access reasons (private or nonexistent repos look identical to an unauthenticated client), automatically retry over SSH as the current user.
• SSH is run with BatchMode=yes and StrictHostKeyChecking=accept-new so the worker never hangs on an interactive prompt.
• The Add App dialog documents that private repos are accessed over SSH using the server's configured SSH key.

Accurate clone errors and tag-safe pulls

• Distinguish "revision not found" (remote reachable, branch/tag mistyped) from "can't access repository" and surface the right message for each, instead of burying both inside a generic "Failed to clone or scan repo" wrapper. The endpoint maps the worker's generic 500 to a 400 for these repo problems while preserving other codes (e.g. 503 worker-dead).
• Pulls now fetch the ref and reset --hard FETCH_HEAD instead of origin/<branch>, so updating an app pinned to a tag or commit (not a branch) works correctly. The fetch carries the SSH env so private-repo origins don't prompt.

Canonical, pinned GitHub URLs

• New canonical_github_url (backend) / canonicalGithubUrl (frontend) that fold URLs to a single canonical https form — stripping .git, trailing slashes, and a redundant /tree/main, and converting SSH to https.
• App, listing, and job URLs are canonicalized on write and on lookup, so the same repo always resolves to one stored representation.
• The launch page now matches the user's library by canonical URL identity rather than exact string, fixing apps (e.g. ones added from the catalog) wrongly showing as "not in your library."
• The revision is resolved once, at add time, in the per-user worker (which holds the user's SSH credentials — the shared server process cannot resolve a private repo's default branch) and baked into the stored URL: a repo whose default is e.g. master is stored as .../tree/master, so it dedups against an explicit /tree/master and the URL always names the revision actually cloned. This closes the bare-vs-default-branch dedup hole where the same app could be added twice.
• The branch column records the user's requested revision ("" = took the default at add time) rather than the resolved one; the Revision shown in the dialogs is parsed from the URL. Once added, a revision is fixed — update just re-pulls the stored URL and refreshes the manifest without re-resolving or moving the row. To follow a changed default branch, delete and re-add the app.
• Legacy apps migrated from user_preferences have a NULL branch (their default was never recorded). These are left to track the current default (stored URL returned unchanged, git resolves the default) rather than being wrongly pinned to main; they get pinned the next time the app is re-added.

App naming

• Pixi apps are now named from the pixi.toml project name (falling back to the git repo name, then the directory) instead of repo/branch, which produced poor names like SmartSPIMGlancer/HEAD since a detached-HEAD clone's leaf directory is the revision.
• Jobs and the launch page prefer the user's saved/custom app name (e.g. one chosen when adding from the catalog) over the raw manifest name. The internal job work_dir still uses the manifest name as a stable path identifier.
• Adding an app from the catalog now preserves the publisher's custom name/description rather than overwriting them with the manifest's values.

UI refinements

• Renamed the user-facing "Branch" label to "Revision" (with a "Tag or branch name" helper) to reflect that tags and commits are valid.
• Job Execution box: show the app and entry point together (<app name> — <entry point>), add a separate repository link labeled owner/repo with (branch) appended only for non-default branches, and use a 40/60 (Status/Execution) card layout.
• Show the user's custom app name on the launch and job pages.
• Show an empty-state message ("There are no parameters to set for this app.") when an app has no parameters.
• Add a share/unshare button to My Apps cards; when not shared, it opens the info dialog straight into the share form.
• Add a confirmation dialog when canceling/stopping a job from the jobs list, matching the job detail page (shared CancelJobDialog component).

Tests

• Backend: tests/test_apps.py, tests/test_apps_endpoints.py, tests/test_catalog_endpoints.py, and tests/test_url_migration.py.
• Frontend: frontend/src/__tests__/unitTests/appUrls.test.ts.

Migration note

Running this branch applies two migrations:

• b8e4f1a92c37 canonicalizes existing app/listing/job GitHub URLs in place, dropping rows that would collide with an already-canonical row under the UNIQUE(owner, url, manifest_path) constraint.
• c1f9a4e7b2d8 bakes the resolved revision (from the old branch column) into existing URLs and derives the requested revision from the URL shape, de-duplicating any rows that collapse together. NULL-branch legacy rows are left untouched (and registered as collision winners so known-app rewrites that fold onto them are dropped rather than violating the unique constraint).

Both downgrades are no-ops since canonicalization is lossy.

@StephanPreibisch @JaneliaSciComp/fileglancer