scripts: use capnp store instead of reading markdown directly

Add store_helpers.py with shared helpers that call poc-memory commands
(list-keys, render, journal-tail) instead of globbing ~/.claude/memory/*.md
and parsing section headers.

All 9 Python scripts updated: get_semantic_keys(), get_topic_file_index(),
get_recent_journal(), parse_journal_entries(), read_journal_range(),
collect_topic_stems(), and file preview rendering now go through the store.

This completes the clean switch — no script reads archived markdown files.

scripts/consolidation-agents.py

@@ -64,88 +64,36 @@ def call_sonnet(prompt: str, timeout: int = 600) -> str:
 # ---------------------------------------------------------------------------
 
 def get_recent_journal(n_lines: int = 200) -> str:
-    """Get last N lines of journal."""
-    journal = MEMORY_DIR / "journal.md"
-    if not journal.exists():
-        return ""
-    with open(journal) as f:
-        lines = f.readlines()
-    return "".join(lines[-n_lines:])
+    """Get recent journal entries from the store."""
+    from store_helpers import get_recent_journal as _get_journal
+    # n_lines ≈ 50 entries (rough heuristic: ~4 lines per entry)
+    return _get_journal(n=max(20, n_lines // 4))
 
 
 def get_topic_file_index() -> dict[str, list[str]]:
-    """Build index of topic files and their section headers."""
-    index = {}
-    for md in sorted(MEMORY_DIR.glob("*.md")):
-        name = md.name
-        if name in ("journal.md", "MEMORY.md", "where-am-i.md",
-                     "work-queue.md", "search-testing.md"):
-            continue
-        sections = []
-        try:
-            with open(md) as f:
-                for line in f:
-                    if line.startswith("## "):
-                        sections.append(line.strip())
-        except Exception:
-            pass
-        index[name] = sections
-    return index
+    """Build index of topic files and their section headers from the store."""
+    from store_helpers import get_topic_file_index as _get_index
+    return _get_index()
 
 
 def get_mem_markers() -> list[dict]:
-    """Extract all <!-- mem: --> markers from memory files."""
+    """Get relations from the store (replaces mem marker parsing)."""
+    from store_helpers import get_relations
+    raw = get_relations()
+    # Parse list-edges output into marker-like dicts
     markers = []
-    for md in sorted(MEMORY_DIR.glob("*.md")):
-        if md.name in ("journal.md", "MEMORY.md"):
+    for line in raw.split('\n'):
+        line = line.strip()
+        if not line:
             continue
-        try:
-            content = md.read_text()
-            for match in re.finditer(
-                r'<!-- mem: (.*?) -->', content):
-                attrs = {}
-                for part in match.group(1).split():
-                    if '=' in part:
-                        k, v = part.split('=', 1)
-                        attrs[k] = v
-                attrs['_file'] = md.name
-                markers.append(attrs)
-        except Exception:
-            pass
+        markers.append({"_raw": line})
     return markers
 
 
 def get_topic_summaries(max_chars_per_file: int = 500) -> str:
-    """Get first N chars of each topic file for cross-link scanning."""
-    parts = []
-    for md in sorted(MEMORY_DIR.glob("*.md")):
-        name = md.name
-        if name in ("journal.md", "MEMORY.md", "where-am-i.md",
-                     "work-queue.md", "search-testing.md"):
-            continue
-        try:
-            content = md.read_text()
-            # Get sections and first paragraph of each
-            sections = []
-            current_section = name
-            current_content = []
-            for line in content.split('\n'):
-                if line.startswith("## "):
-                    if current_content:
-                        text = '\n'.join(current_content[:5])
-                        sections.append(f"  {current_section}: {text[:200]}")
-                    current_section = line.strip()
-                    current_content = []
-                elif line.strip():
-                    current_content.append(line.strip())
-            if current_content:
-                text = '\n'.join(current_content[:5])
-                sections.append(f"  {current_section}: {text[:200]}")
-
-            parts.append(f"\n### {name}\n" + '\n'.join(sections[:15]))
-        except Exception:
-            pass
-    return '\n'.join(parts)
+    """Get topic file summaries from the store."""
+    from store_helpers import get_topic_summaries as _get_summaries
+    return _get_summaries(max_chars_per_file)
 
 
 def get_graph_stats() -> str:
@@ -274,16 +222,13 @@ def build_crosslink_prompt() -> str:
 
     marker_text = ""
     for m in markers:
-        f = m.get('_file', '?')
-        mid = m.get('id', '?')
-        links = m.get('links', '')
-        marker_text += f"  {f}#{mid} → links={links}\n"
+        marker_text += f"  {m.get('_raw', '?')}\n"
 
     return f"""You are the Cross-Link Scanner for ProofOfConcept's memory system.
 
 Your job: find MISSING connections between topic files.
 
-## Existing links (from <!-- mem: --> markers)
+## Existing relations (from the memory graph)
 
 {marker_text}
 
@@ -328,15 +273,13 @@ def build_topology_prompt() -> str:
     stats = get_graph_stats()
     topic_index = get_topic_file_index()
 
+    # Get node counts per file from the store
+    from store_helpers import get_topic_file_index as _get_index
+    topic_index = _get_index()
     file_sizes = ""
-    for md in sorted(MEMORY_DIR.glob("*.md")):
-        if md.name in ("journal.md", "MEMORY.md"):
-            continue
-        try:
-            lines = len(md.read_text().split('\n'))
-            file_sizes += f"  {md.name}: {lines} lines\n"
-        except Exception:
-            pass
+    for fname in sorted(topic_index.keys()):
+        n_sections = len(topic_index[fname])
+        file_sizes += f"  {fname}: {n_sections} sections\n"
 
     return f"""You are the Topology Reporter for ProofOfConcept's memory system.