feat(sync): prepare inputs before resolving generated sources

[srnnkls]

Summary

Generated sources were resolved before their input targets deployed, forcing consumers to stage Tropos and Loqui through a second Phora project before running Henia. This adds a native preparation boundary so one root phora.toml / phora.local.toml pair can complete the whole sync:

pre_sync → prepare inputs → post_prepare (Henia) → resolve/deploy .henia outputs → post_sync (Scrut)

• Add phase = "prepare" targets and an ordered, fail-fast post_prepare hook. Imported subtrees inherit the consumer's phase; ordinary targets keep the default deployment phase. Package manifests are composed before preparation, while generated file sources are resolved afterward.
• Keep one registry, journal, and project lock. Phase-scoped reconciliation preserves deployment records during input pruning. Skipped inputs and preparation/build failures stop deployment, retaining unvisited pins, including separate refs of a shared import. Prepared inputs remain available for retry; arbitrary hook side effects are not rolled back.
• Add update --prune for removing obsolete generated links in the same update, and document the declarative Tropos/Henia configuration. Frozen replay and --no-hooks retain their existing policies.
• Recover an empty cache at the locked package commits: ordinary sync fetches missing mirrors before reading imported manifests, while --frozen remains offline. This lets a fresh deployment start with only configuration and pins.

Stacked on #88; base branch: fix/bound-transitive-sources.

Validation

• cargo test --all-targets: 2,222 passed, 0 failed, 1 existing ignored; doctests passed.
• cargo fmt --check and cargo clippy --all-targets -- -D warnings: passed, including the unchanged state-store architecture gate.
• All CLI Scrut suites: 197 passed. Ten new Rust lifecycle regressions cover first-run generation, transitive inputs, failures/retries, conflicts, pruning, separate import refs, configuration merging, physical destination overlap, and recovery after deleting cache, state, prepared inputs and generated output without advancing Tropos or Loqui pins.
• Real Tropos + transitive Loqui + Henia: 112 artifacts built, all four harness contract checks passed, combined dotfiles deployment and frozen replay passed. Dotfiles builds directly from ~/projects/tropos/.worktrees/henia-phora; Phora prepares only Loqui in that checkout, and Henia writes dotfiles’ .henia outputs. The old resources/tropos copy was removed. Canonical Tropos files and existing edits stayed unchanged, Loqui kept its pin, and deployment targets stayed in a temporary home under an OS sandbox. Dotfiles utility regressions: 7 passed.