diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
index 141da325..652cc042 100644
--- a/docs/ARCHITECTURE.md
+++ b/docs/ARCHITECTURE.md
@@ -569,7 +569,7 @@ The vault backend (`src-tauri/src/vault/`) is split into focused submodules:
 | `trash.rs` | `purge_trash` — deletes trashed notes older than 30 days |
 | `rename.rs` | `rename_note` — renames files and updates wikilinks across the vault |
 | `image.rs` | `save_image` — saves base64-encoded attachments with sanitized filenames |
-| `migration.rs` | Frontmatter migration utilities |
+| `migration.rs` | Frontmatter migration: `migrate_is_a_to_type`, `migrate_to_flat_vault` |
 | `config_seed.rs` | Seeds `config/` folder, migrates `AGENTS.md`, repairs missing config files |
 | `getting_started.rs` | Creates the Getting Started demo vault |
 
@@ -611,6 +611,7 @@ The vault backend (`src-tauri/src/vault/`) is split into focused submodules:
 | `purge_trash` | Delete notes trashed >30 days ago |
 | `reload_vault` | Invalidate cache and full rescan from filesystem → `Vec<VaultEntry>` |
 | `reload_vault_entry` | Re-read a single file from disk → `VaultEntry` |
+| `migrate_to_flat_vault` | Move notes from type subfolders to vault root, update wikilinks |
 | `check_vault_exists` | Check if vault path exists |
 | `create_getting_started_vault` | Bootstrap demo vault |
 
diff --git a/src/hooks/useNoteActions.test.ts b/src/hooks/useNoteActions.test.ts
index 18082112..56c56738 100644
--- a/src/hooks/useNoteActions.test.ts
+++ b/src/hooks/useNoteActions.test.ts
@@ -20,6 +20,7 @@ import {
   useNoteActions,
   DEFAULT_TEMPLATES,
   resolveTemplate,
+  slugCollides,
 } from './useNoteActions'
 import type { NoteActionsConfig } from './useNoteActions'
 
@@ -111,6 +112,38 @@ describe('needsRenameOnSave', () => {
   })
 })
 
+describe('slugCollides', () => {
+  it('detects collision with existing filename', () => {
+    const entries = [makeEntry({ filename: 'my-note.md', path: '/vault/my-note.md' })]
+    expect(slugCollides('My Note', entries)).toBe(true)
+  })
+
+  it('returns false when no collision', () => {
+    const entries = [makeEntry({ filename: 'other.md', path: '/vault/other.md' })]
+    expect(slugCollides('My Note', entries)).toBe(false)
+  })
+
+  it('excludes the current note path from collision check', () => {
+    const entries = [makeEntry({ filename: 'my-note.md', path: '/vault/my-note.md' })]
+    expect(slugCollides('My Note', entries, '/vault/my-note.md')).toBe(false)
+  })
+})
+
+describe('resolveNewNote slug collision', () => {
+  it('auto-suffixes slug when collision detected', () => {
+    const entries = [makeEntry({ filename: 'my-project.md', path: '/vault/my-project.md' })]
+    const { entry } = resolveNewNote('My Project', 'Project', '/vault', null, entries)
+    expect(entry.path).toBe('/vault/my-project-2.md')
+    expect(entry.filename).toBe('my-project-2.md')
+  })
+
+  it('skips suffix when no collision', () => {
+    const entries = [makeEntry({ filename: 'other.md', path: '/vault/other.md' })]
+    const { entry } = resolveNewNote('My Project', 'Project', '/vault', null, entries)
+    expect(entry.path).toBe('/vault/my-project.md')
+  })
+})
+
 describe('buildNewEntry', () => {
   it('creates a VaultEntry with correct fields', () => {
     const entry = buildNewEntry({
@@ -190,8 +223,8 @@ describe('entryMatchesTarget', () => {
     expect(entryMatchesTarget(entry, 'mp')).toBe(true)
   })
 
-  it('matches by path suffix (type/slug)', () => {
-    const entry = makeEntry({ path: '/Users/luca/Laputa/project/my-project.md' })
+  it('matches by filename stem from path-style wikilink', () => {
+    const entry = makeEntry({ path: '/Users/luca/Laputa/my-project.md', filename: 'my-project.md' })
     expect(entryMatchesTarget(entry, 'project/my-project')).toBe(true)
   })
 
diff --git a/src/hooks/useNoteActions.ts b/src/hooks/useNoteActions.ts
index 1ce6c158..5fff6a2e 100644
--- a/src/hooks/useNoteActions.ts
+++ b/src/hooks/useNoteActions.ts
@@ -95,6 +95,12 @@ export function needsRenameOnSave(title: string, filename: string): boolean {
   return `${slugify(title)}.md` !== filename
 }
 
+/** Check if a slug would collide with an existing entry's filename. */
+export function slugCollides(title: string, entries: VaultEntry[], excludePath?: string): boolean {
+  const slug = slugify(title)
+  return entries.some(e => e.filename === `${slug}.md` && e.path !== excludePath)
+}
+
 /** Generate a unique "Untitled <type>" name by checking existing entries and pending names. */
 export function generateUntitledName(entries: VaultEntry[], type: string, pending?: Set<string>): string {
   const baseName = `Untitled ${type.toLowerCase()}`
@@ -190,8 +196,16 @@ export function buildNoteContent(title: string, type: string, status: string | n
   return `${lines.join('\n')}\n\n# ${title}\n${body}`
 }
 
-export function resolveNewNote(title: string, type: string, vaultPath: string, template?: string | null): { entry: VaultEntry; content: string } {
-  const slug = slugify(title)
+export function resolveNewNote(title: string, type: string, vaultPath: string, template?: string | null, entries?: VaultEntry[]): { entry: VaultEntry; content: string } {
+  let slug = slugify(title)
+  // Detect slug collision and auto-suffix
+  if (entries) {
+    let counter = 2
+    while (entries.some(e => e.filename === `${slug}.md`)) {
+      slug = `${slugify(title)}-${counter}`
+      counter++
+    }
+  }
   const status = NO_STATUS_TYPES.has(type) ? null : 'Active'
   const entry = buildNewEntry({ path: `${vaultPath}/${slug}.md`, slug, title, type, status })
   return { entry, content: buildNoteContent(title, type, status, template) }
@@ -363,7 +377,7 @@ export function useNoteActions(config: NoteActionsConfig) {
 
   const handleCreateNote = useCallback((title: string, type: string) => {
     const template = resolveTemplate(entries, type)
-    persistNew(resolveNewNote(title, type, config.vaultPath, template))
+    persistNew(resolveNewNote(title, type, config.vaultPath, template, entries))
   }, [entries, persistNew, config.vaultPath])
 
   const handleCreateNoteImmediate = useCallback((type?: string) => {
@@ -372,7 +386,7 @@ export function useNoteActions(config: NoteActionsConfig) {
       const title = generateUntitledName(entries, noteType, pendingNamesRef.current)
       pendingNamesRef.current.add(title)
       const template = resolveTemplate(entries, noteType)
-      const resolved = resolveNewNote(title, noteType, config.vaultPath, template)
+      const resolved = resolveNewNote(title, noteType, config.vaultPath, template, entries)
       openTabWithContent(resolved.entry, resolved.content)
       addEntryWithMock(resolved.entry, resolved.content, addEntry)
       config.trackUnsaved?.(resolved.entry.path)
@@ -389,7 +403,7 @@ export function useNoteActions(config: NoteActionsConfig) {
    *  Returns true on success, false on failure (shows toast on error). */
   const handleCreateNoteForRelationship = useCallback(async (title: string): Promise<boolean> => {
     const template = resolveTemplate(entries, 'Note')
-    const resolved = resolveNewNote(title, 'Note', config.vaultPath, template)
+    const resolved = resolveNewNote(title, 'Note', config.vaultPath, template, entries)
     openTabWithContent(resolved.entry, resolved.content)
     addEntryWithMock(resolved.entry, resolved.content, addEntry)
     try {
diff --git a/src/utils/wikilink.ts b/src/utils/wikilink.ts
index ea6798a8..4940000e 100644
--- a/src/utils/wikilink.ts
+++ b/src/utils/wikilink.ts
@@ -20,23 +20,28 @@ export function wikilinkDisplay(ref: string): string {
 
 /**
  * Unified wikilink resolution: find the VaultEntry matching a wikilink target.
- * Handles pipe syntax, case-insensitive matching, title/alias/filename/path lookup.
+ * Resolution order: filename stem (primary) → alias → title (fallback).
+ * Handles pipe syntax, case-insensitive matching.
  */
 export function resolveEntry(entries: VaultEntry[], rawTarget: string): VaultEntry | undefined {
   const key = rawTarget.includes('|') ? rawTarget.split('|')[0] : rawTarget
   const keyLower = key.toLowerCase()
-  const suffix = '/' + key + '.md'
   const lastSegment = key.split('/').pop() ?? key
   const asWords = lastSegment.replace(/-/g, ' ').toLowerCase()
 
-  return entries.find(e => {
-    if (e.title.toLowerCase() === keyLower) return true
-    if (e.aliases.some(a => a.toLowerCase() === keyLower)) return true
+  // 1. Filename stem match (primary — filename IS identity in flat vault)
+  const byStem = entries.find(e => {
     const stem = e.filename.replace(/\.md$/, '')
-    if (stem.toLowerCase() === keyLower) return true
-    if (e.path.endsWith(suffix)) return true
-    if (stem.toLowerCase() === lastSegment.toLowerCase()) return true
-    if (e.title.toLowerCase() === asWords) return true
-    return false
+    return stem.toLowerCase() === keyLower || stem.toLowerCase() === lastSegment.toLowerCase()
   })
+  if (byStem) return byStem
+
+  // 2. Alias match
+  const byAlias = entries.find(e => e.aliases.some(a => a.toLowerCase() === keyLower))
+  if (byAlias) return byAlias
+
+  // 3. Title match (fallback)
+  return entries.find(e =>
+    e.title.toLowerCase() === keyLower || e.title.toLowerCase() === asWords,
+  )
 }