diff --git a/packages/browseros-agent/apps/server/src/agent/prompt.ts b/packages/browseros-agent/apps/server/src/agent/prompt.ts
index cde9a4737..fbd59767d 100644
--- a/packages/browseros-agent/apps/server/src/agent/prompt.ts
+++ b/packages/browseros-agent/apps/server/src/agent/prompt.ts
@@ -415,8 +415,10 @@ You remember things across sessions using two tiers:
 **Core memory** (\`CORE.md\`) — permanent facts about the user that persist forever.
 Use for: name, job, location, preferences, relationships, recurring projects, important dates.
 - \`memory_read_core\` → read all permanent facts
-- \`memory_save_core\` → save permanent facts
-  **IMPORTANT**: \`memory_save_core\` overwrites the entire file. Always call \`memory_read_core\` first, merge new facts into existing content, then save the full result.
+- \`memory_update_core\` → add or remove facts from core memory
+  Pass \`additions\` (array of new facts) and/or \`removals\` (array of facts to remove by substring match).
+  This tool handles merging internally — you never need to rewrite the full file.
+  Do NOT use \`memory_save_core\` — it is deprecated and risks overwriting all existing memories.
 
 **Daily memory** — short-lived notes stored in daily files (\`YYYY-MM-DD.md\`). Auto-expire after 30 days.
 Use for: what the user worked on today, transient context, meeting notes, draft ideas, things to follow up on.
diff --git a/packages/browseros-agent/apps/server/src/tools/memory/build-toolset.ts b/packages/browseros-agent/apps/server/src/tools/memory/build-toolset.ts
index 76a6f74e9..8f1b2a24f 100644
--- a/packages/browseros-agent/apps/server/src/tools/memory/build-toolset.ts
+++ b/packages/browseros-agent/apps/server/src/tools/memory/build-toolset.ts
@@ -1,8 +1,8 @@
 import type { ToolSet } from 'ai'
 import { createReadCoreTool } from './read-core'
 import { createSoulReadTool } from './read-soul'
-import { createSaveCoreTool } from './save-core'
 import { createMemorySearchTool } from './search'
+import { createUpdateCoreTool } from './update-core'
 import { createSoulUpdateTool } from './update-soul'
 import { createMemoryWriteTool } from './write'
 
@@ -11,7 +11,7 @@ export function buildMemoryToolSet(): ToolSet {
     memory_search: createMemorySearchTool(),
     memory_write: createMemoryWriteTool(),
     memory_read_core: createReadCoreTool(),
-    memory_save_core: createSaveCoreTool(),
+    memory_update_core: createUpdateCoreTool(),
     soul_read: createSoulReadTool(),
     soul_update: createSoulUpdateTool(),
   }
diff --git a/packages/browseros-agent/apps/server/src/tools/memory/save-core.ts b/packages/browseros-agent/apps/server/src/tools/memory/save-core.ts
deleted file mode 100644
index 8a985e5f5..000000000
--- a/packages/browseros-agent/apps/server/src/tools/memory/save-core.ts
+++ /dev/null
@@ -1,22 +0,0 @@
-import { tool } from 'ai'
-import { z } from 'zod'
-import { getCoreMemoryPath } from '../../lib/browseros-dir'
-import { executeWithMetrics, toModelOutput } from '../filesystem/utils'
-
-const TOOL_NAME = 'memory_save_core'
-
-export function createSaveCoreTool() {
-  return tool({
-    description:
-      'Write or update core memories. IMPORTANT: This overwrites the entire core memory file. Always call memory_read_core first, merge your changes into the existing content, then save the full result.',
-    inputSchema: z.object({
-      content: z.string().describe('The full core memory content to save'),
-    }),
-    execute: (params) =>
-      executeWithMetrics(TOOL_NAME, async () => {
-        await Bun.write(getCoreMemoryPath(), params.content)
-        return { text: 'Core memories updated.' }
-      }),
-    toModelOutput,
-  })
-}
diff --git a/packages/browseros-agent/apps/server/src/tools/memory/search.ts b/packages/browseros-agent/apps/server/src/tools/memory/search.ts
index 1a417bd3e..2cf10e90d 100644
--- a/packages/browseros-agent/apps/server/src/tools/memory/search.ts
+++ b/packages/browseros-agent/apps/server/src/tools/memory/search.ts
@@ -28,10 +28,20 @@ async function loadMemoryEntries(): Promise<MemoryEntry[]> {
   for (const file of mdFiles) {
     try {
       const content = await readFile(join(memoryDir, file), 'utf-8')
+
+      // Section-level entries (## delimited blocks)
       const sections = content.split(/^## /m).filter(Boolean)
       for (const section of sections) {
         entries.push({ source: file, content: `## ${section}`.trim() })
       }
+
+      // Line-level entries (individual non-empty lines)
+      for (const line of content.split('\n')) {
+        const trimmed = line.trim()
+        if (trimmed && !trimmed.startsWith('#')) {
+          entries.push({ source: file, content: trimmed })
+        }
+      }
     } catch {
       // skip unreadable files
     }
@@ -84,11 +94,28 @@ export function createMemorySearchTool() {
           }
         }
 
-        const sorted = [...bestScores.entries()]
-          .sort((a, b) => a[1].score - b[1].score)
-          .slice(0, 10)
+        const sorted = [...bestScores.entries()].sort(
+          (a, b) => a[1].score - b[1].score,
+        )
 
-        const formatted = sorted
+        // Deduplicate: skip line-level hits already covered by a
+        // higher-ranked section from the same file.
+        const seenSections: Array<{ source: string; content: string }> = []
+        const deduped: typeof sorted = []
+        for (const item of sorted) {
+          const { source, content } = item[0]
+          const coveredBySection = seenSections.some(
+            (s) => s.source === source && s.content.includes(content),
+          )
+          if (coveredBySection) continue
+          if (content.startsWith('## ')) {
+            seenSections.push({ source, content })
+          }
+          deduped.push(item)
+        }
+
+        const formatted = deduped
+          .slice(0, 10)
           .map(([entry, { score }]) => {
             const relevance = (1 - score).toFixed(2)
             return `[${entry.source}] (relevance: ${relevance})\n${entry.content}`
diff --git a/packages/browseros-agent/apps/server/src/tools/memory/update-core.ts b/packages/browseros-agent/apps/server/src/tools/memory/update-core.ts
new file mode 100644
index 000000000..06c72287b
--- /dev/null
+++ b/packages/browseros-agent/apps/server/src/tools/memory/update-core.ts
@@ -0,0 +1,74 @@
+import { tool } from 'ai'
+import { z } from 'zod'
+import { getCoreMemoryPath } from '../../lib/browseros-dir'
+import { executeWithMetrics, toModelOutput } from '../filesystem/utils'
+
+const TOOL_NAME = 'memory_update_core'
+
+export function createUpdateCoreTool() {
+  return tool({
+    description:
+      'Add or remove facts from core memory. Handles merging internally — you never need to rewrite the full file. Pass additions to store new facts and/or removals to delete facts by substring match.',
+    inputSchema: z.object({
+      additions: z
+        .array(z.string())
+        .optional()
+        .describe('New facts to add to core memory. Each string is one fact.'),
+      removals: z
+        .array(z.string())
+        .optional()
+        .describe(
+          'Facts to remove from core memory. Each string is matched as a case-insensitive substring against existing lines.',
+        ),
+    }),
+    execute: (params) =>
+      executeWithMetrics(TOOL_NAME, async () => {
+        const corePath = getCoreMemoryPath()
+        const file = Bun.file(corePath)
+
+        let existing = ''
+        if (await file.exists()) {
+          existing = await file.text()
+        }
+
+        let lines = existing.split('\n')
+
+        // Remove matching entries
+        let removedCount = 0
+        if (params.removals?.length) {
+          for (const removal of params.removals) {
+            const lower = removal.toLowerCase()
+            const before = lines.length
+            lines = lines.filter((line) => !line.toLowerCase().includes(lower))
+            removedCount += before - lines.length
+          }
+        }
+
+        // Append new facts (skip duplicates)
+        let addedCount = 0
+        if (params.additions?.length) {
+          if (lines.length > 0 && lines[lines.length - 1].trim() !== '') {
+            lines.push('')
+          }
+          for (const fact of params.additions) {
+            const factLower = fact.toLowerCase()
+            const alreadyExists = lines.some((l) =>
+              l.toLowerCase().includes(factLower),
+            )
+            if (!alreadyExists) {
+              lines.push(`- ${fact}`)
+              addedCount++
+            }
+          }
+        }
+
+        const result = `${lines.join('\n').trim()}\n`
+        await Bun.write(corePath, result)
+
+        return {
+          text: `Core memory updated. ${addedCount} fact(s) added, ${removedCount} line(s) removed.`,
+        }
+      }),
+    toModelOutput,
+  })
+}
diff --git a/packages/browseros-agent/apps/server/tests/agent/prompt.test.ts b/packages/browseros-agent/apps/server/tests/agent/prompt.test.ts
index e9d680c10..e0ff94eac 100644
--- a/packages/browseros-agent/apps/server/tests/agent/prompt.test.ts
+++ b/packages/browseros-agent/apps/server/tests/agent/prompt.test.ts
@@ -289,7 +289,7 @@ describe('mode-aware framing', () => {
     // The agent shouldn't even see memory tool instructions.
     const prompt = buildChatMode()
     expect(prompt).not.toContain('<memory_and_identity>')
-    expect(prompt).not.toContain('memory_save_core')
+    expect(prompt).not.toContain('memory_update_core')
     expect(prompt).not.toContain('soul_update')
   })
 
@@ -687,17 +687,25 @@ describe('memory and identity', () => {
     const prompt = buildRegular()
     expect(prompt).toContain('memory_search')
     expect(prompt).toContain('memory_write')
-    expect(prompt).toContain('memory_save_core')
+    expect(prompt).toContain('memory_update_core')
     expect(prompt).toContain('memory_read_core')
   })
 
-  it('includes critical overwrite warning for memory_save_core', () => {
-    // Why: memory_save_core overwrites the entire file. Without the
-    // "read first, merge, then save" instruction, the agent will
-    // silently destroy existing memories when saving new ones.
+  it('discourages use of deprecated memory_save_core', () => {
+    // Why: memory_save_core overwrites the entire file and risks data loss.
+    // The prompt must steer the agent to memory_update_core instead.
     const prompt = buildRegular()
-    expect(prompt).toContain('memory_save_core` overwrites the entire file')
-    expect(prompt).toContain('Always call `memory_read_core` first')
+    expect(prompt).toContain('Do NOT use `memory_save_core`')
+    expect(prompt).toContain('deprecated')
+  })
+
+  it('explains memory_update_core merge-based API', () => {
+    // Why: The agent must understand that memory_update_core handles merging
+    // internally via additions/removals — it should never rewrite the full file.
+    const prompt = buildRegular()
+    expect(prompt).toContain('additions')
+    expect(prompt).toContain('removals')
+    expect(prompt).toContain('handles merging internally')
   })
 
   it('explains two-tier memory model with core and daily distinction', () => {