Update verilib-cli for Probe Schema 2.0 envelope and folder restructure

[astefano]

Context

We are introducing Schema 2.0 for probe output files (probe-lean, probe-verus). The key changes are:

1. Envelope wrapper: All probe JSON outputs will be wrapped in a metadata envelope instead of being bare dictionaries. The envelope contains schema, schema-version, tool (name, version, command), source (repo, commit, language, package, package-version), timestamp, and data.

2. Folder restructure: The flat .verilib/ layout is being reorganized into subdirectories:

Current:

.verilib/
  config.json
  atoms.json
  specs.json
  proofs.json
  stubs.json
  graph.json
  structure/

Proposed:

.verilib/
  config.json
  probes/
    lean_<package>_<version>.json
    verus_<package>_<version>.json
  views/
    molecule_all.json          (replaces stubs.json)
    package_all.json
  translations/
    verus_dalek__lean_dalek.json

What needs to change in verilib-cli

1. Read enveloped probe outputs

All code that reads atoms.json, specs.json, proofs.json needs to:

• Expect the data under a "data" key inside an envelope object
• Optionally validate schema and schema-version fields for compatibility
• Read from probes/ subdirectory instead of flat .verilib/ root

Affected files:

• src/commands/atomize.rs (reads atoms.json)
• src/commands/specify.rs (reads specs.json)
• src/commands/verify.rs (reads proofs.json)
• src/config.rs (atoms_path(), stubs_path(), verilib_path())

2. Write to new folder structure

• init should create probes/, views/, translations/ subdirectories
• Output paths should target the new locations
• deploy should scan the new folder structure

3. Use envelope metadata for staleness detection

The source.commit and timestamp fields in the envelope enable checking whether probe outputs are stale relative to the current repo HEAD. This supports the workflow: "commit before atomize/specify/verify; if not committed, regenerate everything."

4. Views replace stubs

stubs.json becomes a "view" in views/molecule_all.json. The stubify concept evolves into a filtered projection of probe data.

Design documents

• Generic envelope rationale: Add Schema 2.0 envelope rationale probe#1
• Lean-specific instantiation: Add Schema 2.0 Lean instantiation spec probe-lean#2

Notes

• No backward compatibility period needed -- probe tools and verilib-cli are updated in lockstep
• Each probe file is self-describing via its envelope, so verilib-cli can dispatch on content rather than filename/path
• The filename convention <language>_<package>_<version>.json is for human convenience; code should read the envelope