Apps refactor

[krokicki]

Refactor: split apps/core.py into cohesive modules

Why

fileglancer/apps/core.py had grown to 1701 lines, mixing nine unrelated
concerns behind a flat list of module-level functions. It was hard to navigate,
hard to test in isolation, and a magnet for further growth.

This PR splits it into four single-purpose modules and deletes core.py
(clean break). It is a pure reorganization — no behavior change.

New structure

graph TD
    subgraph consumers["External consumers"]
        server["server.py"]
        worker["user_worker.py"]
        tests["tests/"]
    end

    init["apps/__init__.py<br/><i>re-exports public API</i>"]

    subgraph pkg["fileglancer/apps/"]
        manifest["manifest.py<br/><i>worker dispatch + git repo<br/>cache + manifest discovery/loading</i>"]
        command["command.py<br/><i>requirement checks + path/param<br/>validation + build_command</i>"]
        jobfiles["jobfiles.py<br/><i>work-dir path construction<br/>+ job file access</i>"]
        jobs["jobs.py<br/><i>poll loop + job<br/>submission/cancel</i>"]
        adapters["adapters.py / pixi.py / nextflow.py<br/><i>manifest adapters (unchanged)</i>"]
    end

    server --> init
    worker --> init
    tests --> init

    init --> manifest
    init --> command
    init --> jobfiles
    init --> jobs

    jobs --> manifest
    jobs --> command
    jobs --> jobfiles

    manifest --> adapters

    classDef leaf fill:#e8f4ea,stroke:#3a7d44;
    classDef orchestrator fill:#e7eefc,stroke:#2f5fb0;
    classDef facade fill:#fdf3e3,stroke:#c08a2d;
    class manifest,command,jobfiles leaf;
    class jobs orchestrator;
    class init facade;

Loading

The module graph is a DAG: jobs is the only module with sibling
dependencies; manifest, command, and jobfiles are independent leaves.
No circular-import risk.

Module responsibilities

Module	Responsibility	~lines
manifest.py	worker dispatch (_dispatch/set_worker_exec), git repo cache, manifest discovery & DB-cache loading	430
command.py	requirement-check generation, path/parameter validation, build_command	390
jobs.py	background poll loop, job submission & cancellation	700
jobfiles.py	work-dir path construction, job file access	200

Intra-package edges

flowchart LR
    jobs -->|"_dispatch, _ensure_repo_cache,<br/>get_or_load_manifest"| manifest
    jobs -->|"build_command, merge_requirements,<br/>build_requirements_check"| command
    jobs -->|"_build_work_dir"| jobfiles
    manifest -->|"try_adapt, MANIFEST_ADAPTERS"| adapters

Loading

External dependencies (outside the package): all four touch database;
manifest/jobs/jobfiles touch settings; command touches filestore;
jobs touches cluster_api.

Backward compatibility

• apps/__init__.py re-exports the same public names, so package-level access
  (fileglancer.apps.X) is unchanged — server.py needed no edits.
• user_worker.py inline imports were repointed to the new modules.
• Test imports and patch(...) targets were repointed to the module that now
  owns each name (e.g. apps.core._dispatch → apps.jobs._dispatch,
  apps.core.fetch_app_manifest → apps.manifest.fetch_app_manifest).

Verification

• Full backend suite: 382 passed.
• import fileglancer.apps / server / user_worker is clean (no circular imports).
• grep -rn "apps\.core" returns nothing — the clean break is complete.

@StephanPreibisch @JaneliaSciComp/fileglancer