From 6340901c9ca1f97d38d504b7b74cb121fe16572e Mon Sep 17 00:00:00 2001
From: Chaos <chaos@local>
Date: Tue, 4 Aug 2026 10:56:42 +0200
Subject: [PATCH] fix: exclude superseded memories from recall and classify all
 markdown as docs

Two bugs in the memory and RAG indexers:

1. recall (internal/memory/read.go): entries marked as superseded_by
   (e.g. after a merge) were still returned as top semantic matches.
   They now stay invisible to recall while remaining visible to
   List/ListLightweight for maintenance tools.

2. markdown classification (internal/rag/documents.go): classifySourceType
   received empty content, so a plain .md file (not README, not under
   docs/) fell through and was silently skipped with 0 chunks. Every .md
   file is now classified as 'docs'. Adds regression test cases.
---
 .gitignore                | 1 +
 internal/memory/read.go   | 8 ++++++++
 internal/rag/documents.go | 4 +---
 internal/rag/rag_test.go  | 2 ++
 4 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index a069947..f9882f3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,3 +23,4 @@ logs/
 
 # Go
 vendor/
+agent-memory-mcp-new
diff --git a/internal/memory/read.go b/internal/memory/read.go
index 98b9c77..dd7a17f 100644
--- a/internal/memory/read.go
+++ b/internal/memory/read.go
@@ -197,6 +197,14 @@ func (ms *Store) Recall(ctx context.Context, query string, filters Filters, limi
 			continue
 		}
 
+		// Superseded entries (temporal replacement, e.g. after a merge) are
+		// invisible to semantic recall — the successor carries the current
+		// knowledge. Kept in the DB for temporal history; List/ListLightweight
+		// still return them for maintenance tools.
+		if m.SupersededBy != "" {
+			continue
+		}
+
 		// T48 layer-aware filtering: when the flag is on, surface memories
 		// are invisible outside their originating Context. This prevents
 		// session scratch state from leaking into unrelated recall calls.
diff --git a/internal/rag/documents.go b/internal/rag/documents.go
index b15c3da..a5991db 100644
--- a/internal/rag/documents.go
+++ b/internal/rag/documents.go
@@ -237,9 +237,7 @@ func classifySourceType(docPath string, title string, content string) string {
 			return "k8s"
 		}
 	case ext == ".md":
-		if baseLower == "readme.md" || strings.HasPrefix(pathLower, "docs/") || strings.Contains(pathLower, "/docs/") || strings.Contains(contentLower, "# ") {
-			return "docs"
-		}
+		return "docs"
 	case ext == ".yaml" || ext == ".yml":
 		if strings.Contains(contentLower, "apiVersion:") && strings.Contains(contentLower, "kind:") {
 			return "k8s"
diff --git a/internal/rag/rag_test.go b/internal/rag/rag_test.go
index 85e2002..8fef67a 100644
--- a/internal/rag/rag_test.go
+++ b/internal/rag/rag_test.go
@@ -569,6 +569,8 @@ func TestClassifySourceType(t *testing.T) {
 		{path: "k8s/ingress.yaml", want: "k8s"},
 		{path: "dead_ends/why-we-avoid-async-migration.md", want: "dead_end"},
 		{path: "notes/why-we-avoid-shared-mutable-state.md", want: "dead_end"},
+		{path: "knowledge/mahoo-architecture.md", want: "docs"},
+		{path: "plans/analysis.md", want: "docs"},
 	}
 
 	for _, tc := range tests {