Adopt DataVault v0.4.0 with run hierarchy and log.toml discovery (v0.3.0)

[sotashimozono]

Summary

Adopt DataVault v0.4.0:

• DataVault v0.3.0 added a `run` segment in the data layout (`data/{project}/{run}/...`) and a frozen `.datavault/{project}/{run}.log.toml` discovery anchor.
• DataVault v0.4.0 added the `attach` / `open_all` programmatic query API.

Changes

• Pin `[sources]` to `rev = "main"` so `Pkg.update` tracks upstream
• Update `data separation: config_snapshot.toml` test for the run-segmented path (`data/{project}/{run}/config_snapshot.toml`)
• Add a new test asserting that the log.toml discovery anchor and the `.datavault/README.md` warning are emitted on `Vault` construction
• Bump `DynamicalModels` to v0.3.0

Test plan

• `julia --project=. test/runtests.jl` → 451/451 pass
• End-to-end demo: 18 Lorenz computations under `Vault(...; run="pilot")`, all marked done, ledger built
• Vault-side `reconcile.jl` discovers `apps/DynamicalModels.jl/out/.datavault/lorenz_rho_sweep/pilot.log.toml` and aggregates 18 ledger rows into `master_ledger.csv`
• Vault-side `search.jl --status done` returns the 18 rows with correct `app/project_name/run` columns

[codecov]

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