fix(incremental): scoped --update <subfolder> silently prunes the rest of the graph

[tduong628]

The bug

Running graphify <subfolder> --update on a subfolder of a corpus that is rooted higher up silently deletes every node outside that subfolder.

detect_incremental() computes deletions as:

current_files = {f for flist in full["files"].values() for f in flist}
deleted_files = [f for f in manifest if f not in current_files]

current_files only contains paths under the scanned root, so every manifest entry outside root is reported as deleted. The skill's --update flow forwards that list straight to build_merge(prune_sources=...):

deleted = list(incremental.get('deleted_files', []))
G = build_merge([new_extraction], graph_path='graphify-out/graph.json', prune_sources=deleted or None)

…and build_merge's anti-shrink safety check (#479) is explicitly skipped whenever prune_sources is set, so there is no guardrail — the rest of the graph is wiped with no error.

Repro

A graph built from a corpus root containing memory/ and topics/. Later, graphify topics/ --update to fold in one new topic file. Result: all memory/ nodes are reported deleted and pruned. (Hit this in practice: a scoped update on a topics folder reported ~250 unrelated nodes as deleted.)

The fix

detect_incremental() now treats a manifest entry as deleted only when it is (a) inside the current scan root's subtree AND (b) genuinely absent from disk. Out-of-scope entries are simply not part of this incremental run, and entries still on disk but skipped by detect() (sensitive / unsupported / excluded) are not deletions either.

Two supporting changes:

• realpath-based manifest matching so symlink / mount-alias / .. path-form drift no longer produces false changed or false deleted.
• a loud, non-raising warning in build_merge when a prune would remove a large share of the graph — defense in depth, since the disabled anti-shrink guard is what made the original failure silent.

Tests

New tests/test_incremental_scope_safety.py (4 cases):

• scoped subfolder update reports no out-of-scope deletions
• genuine in-scope deletion is still detected
• full-root update still prunes genuinely deleted files
• a manifest file still present on disk is never reported deleted

tests/test_incremental_scope_safety.py ....                    [100%]
4 passed

No regressions: test_detect.py, test_incremental.py, test_build.py → 140 passed.