`codegraph index` ran extraction against the already-populated DB without
clearing it first. On an unchanged tree every file's content hash still
matched, so the orchestrator skipped re-inserting all of them and the run
reported its delta (after - before = 0) as "0 nodes, 0 edges" — which read as
if `index` had wiped the graph. `init` only ever differed because it runs on a
freshly created, empty DB.
Clear the existing graph before re-indexing so `index` rebuilds from scratch
and reports the same complete result as a fresh `init`. `--force` keeps its
role as the home-dir/root-path override; `sync` stays the incremental path.
Adds an end-to-end regression test driving the built binary (init -> index),
asserting the graph stays populated and the summary is never "0 nodes, 0 edges".
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
