fix(detect): honor .graphifyignore for the memory tree (fixes #2267)

[Munawarx]

Problem

.graphifyignore patterns are silently bypassed for graphify-out/memory/, so users cannot exclude their own saved Q&A output from the corpus. The tree gets re-ingested on every run and node counts grow for reasons unrelated to the source tree.

Root cause

In graphify/detect.py the ignore check is guarded:

if not in_memory and _is_ignored(p, root, ignore_patterns, _cache=ignore_cache):
    ignored.append(str(p)); continue

The not in_memory condition means user ignore patterns never apply to the memory tree. This is issue #2267, Option 1 (the maintainer-friendly fix the reporter requested).

Solution

Remove the not in_memory guard so _is_ignored applies to the memory tree like every other path. Default behavior is unchanged: memory is still ingested unless explicitly ignored.

As a side benefit, the hidden/noise filter (which also keyed off in_memory) now correctly applies to the memory tree, so stray dotfiles dropped there are no longer unconditionally picked up.

Testing

• Added test_graphifyignore_excludes_memory_tree in tests/test_detect.py (matches existing style, uses tmp_path).
• Verified the test FAILS on the unfixed code and PASSES with the fix.
• Regression: with no .graphifyignore, memory is still ingested (default loop intact).
• Edge cases checked: parent pattern graphify-out/, nested proj/graphify-out/memory/, and negation patterns behave correctly.

Expected impact

Users can finally scope the graph to the source tree only. Removes silent config-ignored behavior.

Fixes #2267

[safishamsi]

Thanks @Munawarx — the gap is real (user ignore patterns never reach graphify-out/memory/). But the one-line change over-reaches: ignore_patterns includes .gitignore and $GIT_DIR/info/exclude, not just .graphifyignore. Since graphify-out/ is generated output and is commonly gitignored, dropping the guard silently disables the memory round-trip by default for those repos — I verified _is_ignored(<root>/graphify-out/memory/query_1.md, ...) returns True with graphify-out/ in .gitignore, which contradicts the 'default unchanged' claim. Please scope this to .graphifyignore-sourced patterns only (track pattern provenance and apply just those to the memory tree), and add a regression test that a gitignored graphify-out/ still keeps memory included. Happy to re-review.