diff --git a/CHANGELOG.md b/CHANGELOG.md
index 98f81ce4..db243ca9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -64,6 +64,16 @@ PyPI version — not the changelog header.
   a step to audit every open todo against the actual system (`ls`/`find`/`git
   ls-files`/`grep`/`audit`) and close what's verifiably done — catching todos
   finished in a past session but never closed.
+- **Backup ignore architecture documented** — confirmed and written down the
+  two-layer model so it stops getting re-discovered: `BUILTIN_IGNORES` is the
+  **seed** that generates a new project's `.backupignore` at register and is
+  never consulted at backup time; `.backupignore` (via `load_spec`) is the
+  **runtime source of truth**. There's no static fallback, so the seed is
+  safety-critical — an empty `.backupignore` backs up everything and can crash
+  the machine. Added a "How Ignores Work" README section + code comments on
+  `BUILTIN_IGNORES` and `load_spec`. Also added `logs/` to the seed so new
+  projects exclude log directories (e.g. prax `.jsonl` output) by default, not
+  just `*.log` files (td-27).
 
 ## [2026-06-23]
 
diff --git a/src/aipass/backup/README.md b/src/aipass/backup/README.md
index c130fadf..000dadb2 100644
--- a/src/aipass/backup/README.md
+++ b/src/aipass/backup/README.md
@@ -105,15 +105,17 @@ The root `.gitignore` covers all three with a single `.backup/` entry.
 
 ---
 
-## `.backupignore`
+## How Ignores Work
 
-A true `.gitignore` for backups, using real pathspec/gitwildmatch semantics:
-- `#` comments, blank lines ignored
-- `!` negation (un-ignore a path)
-- Trailing `/` for directory-only matching
-- Last-match-wins ordering
+Two layers — seed and runtime:
 
-Lives at the **project root** and is the single source of truth governing snapshot, versioned, Drive sync, and mirror-cleanup operations. Generated from `BUILTIN_IGNORES` in `handlers/ignore/patterns.py` during `register`. The `.backup/` directory is included in `BUILTIN_IGNORES`, so the store self-excludes from its own backups.
+1. **`BUILTIN_IGNORES`** (`handlers/ignore/patterns.py`) — the **seed**. Written into a new project's `.backupignore` at `register` time (`setup._build_backupignore()`). Never consulted at backup time.
+2. **`.backupignore`** — the **runtime source of truth**. `load_spec()` reads it on every backup; `BUILTIN_IGNORES` is not applied. True pathspec/gitwildmatch semantics: `#` comments, `!` negation, trailing `/` for dirs, last-match-wins.
+
+There is no static fallback. The seed IS the safety mechanism — an empty or missing `.backupignore` means back up everything (`.venv`, `node_modules`, `.git`), which can crash the machine. Keep `BUILTIN_IGNORES` sane.
+
+- To change defaults for **new** projects → edit `BUILTIN_IGNORES` in `patterns.py`
+- To change ignores for an **existing** project → edit its `.backupignore`
 
 The repo-root `/.backupignore` ships intentionally as the curated default so users don't snapshot junk.
 
diff --git a/src/aipass/backup/apps/handlers/ignore/patterns.py b/src/aipass/backup/apps/handlers/ignore/patterns.py
index f77ad88a..f85876c8 100644
--- a/src/aipass/backup/apps/handlers/ignore/patterns.py
+++ b/src/aipass/backup/apps/handlers/ignore/patterns.py
@@ -17,6 +17,9 @@ import pathspec
 from ..json import json_handler
 from ..path import builder
 
+# Seed for new-project .backupignore (written at register by setup._build_backupignore).
+# NOT applied at backup time — runtime ignores come from .backupignore via load_spec().
+# Keep sane: empty seed = back up everything = crash.
 BUILTIN_IGNORES = [
     ".backup/",
     ".git/",
@@ -40,6 +43,7 @@ BUILTIN_IGNORES = [
     "build/",
     "dist/",
     "*.log",
+    "logs/",
     ".ruff_cache/",
     ".coverage",
 ]
@@ -48,6 +52,7 @@ BUILTIN_IGNORES = [
 def load_spec(project_root: str) -> pathspec.PathSpec:
     """Load a PathSpec from .backupignore at the project root.
 
+    This is the runtime source of truth — BUILTIN_IGNORES is not consulted here.
     Reads raw lines — pathspec handles #comments, blanks, !negation,
     anchoring, dir-only trailing /, and last-match-wins natively.
 
diff --git a/src/aipass/backup/tests/test_ignore_pathspec.py b/src/aipass/backup/tests/test_ignore_pathspec.py
index d96b9d25..6b0a03bc 100644
--- a/src/aipass/backup/tests/test_ignore_pathspec.py
+++ b/src/aipass/backup/tests/test_ignore_pathspec.py
@@ -250,6 +250,10 @@ class TestSeedTemplate:
         """Seed defaults include .coverage."""
         assert ".coverage" in BUILTIN_IGNORES
 
+    def test_builtin_has_logs_dir(self):
+        """Seed defaults exclude logs/ directories."""
+        assert "logs/" in BUILTIN_IGNORES
+
     def test_build_backupignore_content(self):
         """Seed template includes ruff_cache, coverage, and pycache."""
         from aipass.backup.apps.handlers.project.setup import _build_backupignore