diff --git a/tdn-desktop/src-tauri/src/vault/manager.rs b/tdn-desktop/src-tauri/src/vault/manager.rs
index cb9baabe..a308bac2 100644
--- a/tdn-desktop/src-tauri/src/vault/manager.rs
+++ b/tdn-desktop/src-tauri/src/vault/manager.rs
@@ -95,19 +95,25 @@ impl VaultIndex {
         self.areas.get(id)
     }
 
-    /// Get all tasks
+    /// Get all tasks, sorted alphabetically by title for deterministic ordering.
     pub fn all_tasks(&self) -> Vec<Task> {
-        self.tasks.values().cloned().collect()
+        let mut tasks: Vec<Task> = self.tasks.values().cloned().collect();
+        tasks.sort_by_cached_key(|t| t.title.to_lowercase());
+        tasks
     }
 
-    /// Get all projects
+    /// Get all projects, sorted alphabetically by title for deterministic ordering.
     pub fn all_projects(&self) -> Vec<Project> {
-        self.projects.values().cloned().collect()
+        let mut projects: Vec<Project> = self.projects.values().cloned().collect();
+        projects.sort_by_cached_key(|p| p.title.to_lowercase());
+        projects
     }
 
-    /// Get all areas
+    /// Get all areas, sorted alphabetically by title for deterministic ordering.
     pub fn all_areas(&self) -> Vec<Area> {
-        self.areas.values().cloned().collect()
+        let mut areas: Vec<Area> = self.areas.values().cloned().collect();
+        areas.sort_by_cached_key(|a| a.title.to_lowercase());
+        areas
     }
 
     /// Update a task in the index
@@ -875,39 +881,48 @@ mod tests {
     // ------------------------------------------------------------------------
 
     #[test]
-    fn vault_index_all_tasks() {
+    fn vault_index_all_tasks_sorted_alphabetically() {
         let tasks = vec![
-            test_task("task-1", "/tasks/task-1.md"),
-            test_task("task-2", "/tasks/task-2.md"),
+            test_task("z", "/tasks/z.md"),
+            test_task("a", "/tasks/a.md"),
+            test_task("m", "/tasks/m.md"),
         ];
         let index = VaultIndex::from_scans(tasks, vec![], vec![]);
 
         let all = index.all_tasks();
-        assert_eq!(all.len(), 2);
+        assert_eq!(all.len(), 3);
+        let titles: Vec<&str> = all.iter().map(|t| t.title.as_str()).collect();
+        assert_eq!(titles, vec!["Task a", "Task m", "Task z"]);
     }
 
     #[test]
-    fn vault_index_all_projects() {
+    fn vault_index_all_projects_sorted_alphabetically() {
         let projects = vec![
-            test_project("proj-1", "/projects/proj-1.md"),
-            test_project("proj-2", "/projects/proj-2.md"),
+            test_project("z", "/projects/z.md"),
+            test_project("a", "/projects/a.md"),
+            test_project("m", "/projects/m.md"),
         ];
         let index = VaultIndex::from_scans(vec![], projects, vec![]);
 
         let all = index.all_projects();
-        assert_eq!(all.len(), 2);
+        assert_eq!(all.len(), 3);
+        let titles: Vec<&str> = all.iter().map(|p| p.title.as_str()).collect();
+        assert_eq!(titles, vec!["Project a", "Project m", "Project z"]);
     }
 
     #[test]
-    fn vault_index_all_areas() {
+    fn vault_index_all_areas_sorted_alphabetically() {
         let areas = vec![
-            test_area("area-1", "/areas/area-1.md"),
-            test_area("area-2", "/areas/area-2.md"),
+            test_area("z", "/areas/z.md"),
+            test_area("a", "/areas/a.md"),
+            test_area("m", "/areas/m.md"),
         ];
         let index = VaultIndex::from_scans(vec![], vec![], areas);
 
         let all = index.all_areas();
-        assert_eq!(all.len(), 2);
+        assert_eq!(all.len(), 3);
+        let titles: Vec<&str> = all.iter().map(|a| a.title.as_str()).collect();
+        assert_eq!(titles, vec!["Area a", "Area m", "Area z"]);
     }
 
     // ------------------------------------------------------------------------
diff --git a/tdn-desktop/src/components/kanban/AreaKanbanBoard.tsx b/tdn-desktop/src/components/kanban/AreaKanbanBoard.tsx
index ae7100f0..209b348c 100644
--- a/tdn-desktop/src/components/kanban/AreaKanbanBoard.tsx
+++ b/tdn-desktop/src/components/kanban/AreaKanbanBoard.tsx
@@ -4,6 +4,7 @@ import { useDroppable } from '@dnd-kit/core'
 import { SortableContext, verticalListSortingStrategy } from '@dnd-kit/sortable'
 
 import { cn } from '@/lib/utils'
+import { matchesWikilinkTitle } from '@/lib/wikilink'
 import type { Task, TaskStatus, Project } from '@/lib/tauri-bindings'
 import { taskStatusConfig } from '@/config/status'
 import { SortableKanbanCard } from './KanbanColumn'
@@ -168,7 +169,7 @@ export function AreaKanbanBoard({
             }
             // swimlaneId is a project ID - find the project and check if task.project matches
             const project = projects.find(p => p.id === swimlaneId)
-            return project && t.project?.includes(project.title)
+            return project && matchesWikilinkTitle(t.project, project.title)
           })
           onTasksReorder(swimlaneId, status, swimlaneTasks)
         }
diff --git a/tdn-desktop/src/components/views/AreaView.tsx b/tdn-desktop/src/components/views/AreaView.tsx
index 7691eef0..5dabd8e5 100644
--- a/tdn-desktop/src/components/views/AreaView.tsx
+++ b/tdn-desktop/src/components/views/AreaView.tsx
@@ -12,6 +12,7 @@ import { useDisplayOrderStore } from '@/store/display-order-store'
 import type { Task, TaskStatus, Project } from '@/lib/tauri-bindings'
 import { useTaskDetailStore } from '@/store/task-detail-store'
 import { useCommandContext } from '@/hooks/use-command-context'
+import { matchesWikilinkTitle } from '@/lib/wikilink'
 import { showTaskContextMenu, showProjectContextMenu } from '@/lib/context-menu'
 import { useTaskCreationStore } from '@/store/task-creation-store'
 import { useNavigationStore } from '@/store/navigation-store'
@@ -167,7 +168,7 @@ export function AreaView({ areaId }: AreaViewProps) {
     // Add regular project tasks with stored order applied
     for (const project of areaProjects) {
       const rawProjectTasks = tasks.filter(t =>
-        t.project?.includes(project.title)
+        matchesWikilinkTitle(t.project, project.title)
       )
       const storedOrder = projectTaskOrder?.[project.id] ?? null
       const orderedProjectTasks = applyStoredOrder(rawProjectTasks, storedOrder)
@@ -188,7 +189,9 @@ export function AreaView({ areaId }: AreaViewProps) {
     // Collect all tasks from projects and loose tasks
     const allTasks = [...orderedLooseTasks]
     for (const project of areaProjects) {
-      const projectTasks = tasks.filter(t => t.project?.includes(project.title))
+      const projectTasks = tasks.filter(t =>
+        matchesWikilinkTitle(t.project, project.title)
+      )
       allTasks.push(...projectTasks)
     }
     for (const task of allTasks) {
diff --git a/tdn-desktop/src/components/views/NoAreaView.tsx b/tdn-desktop/src/components/views/NoAreaView.tsx
index 02ddc795..1590d757 100644
--- a/tdn-desktop/src/components/views/NoAreaView.tsx
+++ b/tdn-desktop/src/components/views/NoAreaView.tsx
@@ -8,6 +8,7 @@ import {
   useCreateTask,
   useDeleteTask,
 } from '@/services/vault'
+import { matchesWikilinkTitle } from '@/lib/wikilink'
 import { useDisplayOrderStore } from '@/store/display-order-store'
 import type { Task, TaskStatus } from '@/lib/tauri-bindings'
 import { useTaskDetailStore } from '@/store/task-detail-store'
@@ -133,7 +134,7 @@ export function NoAreaView() {
     // Add regular project tasks with stored order applied
     for (const project of orphanProjects) {
       const rawProjectTasks = tasks.filter(t =>
-        t.project?.includes(project.title)
+        matchesWikilinkTitle(t.project, project.title)
       )
       const storedOrder = projectTaskOrder?.[project.id] ?? null
       const orderedProjectTasks = applyStoredOrder(rawProjectTasks, storedOrder)
@@ -154,7 +155,9 @@ export function NoAreaView() {
     // Collect all tasks from projects and orphan tasks
     const allTasks = [...orderedOrphanTasks]
     for (const project of orphanProjects) {
-      const projectTasks = tasks.filter(t => t.project?.includes(project.title))
+      const projectTasks = tasks.filter(t =>
+        matchesWikilinkTitle(t.project, project.title)
+      )
       allTasks.push(...projectTasks)
     }
     for (const task of allTasks) {
diff --git a/tdn-desktop/src/components/views/ProjectView.tsx b/tdn-desktop/src/components/views/ProjectView.tsx
index 0aa1510d..be2ba90b 100644
--- a/tdn-desktop/src/components/views/ProjectView.tsx
+++ b/tdn-desktop/src/components/views/ProjectView.tsx
@@ -6,7 +6,7 @@ import {
   useCreateTask,
   useDeleteTask,
 } from '@/services/vault'
-import { stripWikilink } from '@/lib/wikilink'
+import { matchesWikilinkTitle, stripWikilink } from '@/lib/wikilink'
 import type { Task, TaskStatus } from '@/lib/tauri-bindings'
 import { useTaskDetailStore } from '@/store/task-detail-store'
 import { useCommandContext } from '@/hooks/use-command-context'
@@ -70,7 +70,7 @@ export function ProjectView({ projectId }: ProjectViewProps) {
   // So we match using the project's title, not its ID
   const projectTasks = React.useMemo(() => {
     if (!project) return []
-    return tasks.filter(t => t.project?.includes(project.title))
+    return tasks.filter(t => matchesWikilinkTitle(t.project, project.title))
   }, [tasks, project])
 
   // Build tasksByStatus map for kanban view
diff --git a/tdn-desktop/src/components/views/TodayView.tsx b/tdn-desktop/src/components/views/TodayView.tsx
index 5d93de5e..f4cdcb9a 100644
--- a/tdn-desktop/src/components/views/TodayView.tsx
+++ b/tdn-desktop/src/components/views/TodayView.tsx
@@ -11,6 +11,7 @@ import {
 import type { Task } from '@/lib/tauri-bindings'
 import { useTaskDetailStore } from '@/store/task-detail-store'
 import { useTaskCreationStore } from '@/store/task-creation-store'
+import { matchesWikilinkTitle } from '@/lib/wikilink'
 import { useTodayOrder, type TodaySectionId } from '@/hooks/use-today-order'
 import { SectionTaskGroup } from '@/components/tasks/SectionTaskGroup'
 import { TaskDndContext } from '@/components/tasks/TaskDndContext'
@@ -118,16 +119,16 @@ export function TodayView() {
   )
 
   // Get context name (project/area) for a task
-  // Note: task.project and task.area are WikiLink format (e.g., "[[My Project]]")
-  // so we match against the title using includes()
   const getTaskContextName = React.useCallback(
     (task: Task): string | undefined => {
       if (task.project) {
-        const project = projects.find(p => task.project?.includes(p.title))
+        const project = projects.find(p =>
+          matchesWikilinkTitle(task.project, p.title)
+        )
         return project?.title
       }
       if (task.area) {
-        const area = areas.find(a => task.area?.includes(a.title))
+        const area = areas.find(a => matchesWikilinkTitle(task.area, a.title))
         return area?.title
       }
       return undefined
diff --git a/tdn-desktop/src/components/views/WeekView.tsx b/tdn-desktop/src/components/views/WeekView.tsx
index 4658a715..78ee3216 100644
--- a/tdn-desktop/src/components/views/WeekView.tsx
+++ b/tdn-desktop/src/components/views/WeekView.tsx
@@ -2,7 +2,7 @@ import * as React from 'react'
 import { startOfWeek, endOfWeek, isWithinInterval, parseISO } from 'date-fns'
 
 import { useVaultData, useUpdateTask, useCreateTask } from '@/services/vault'
-import { stripWikilink } from '@/lib/wikilink'
+import { matchesWikilinkTitle, stripWikilink } from '@/lib/wikilink'
 import type { Task, TaskStatus } from '@/lib/tauri-bindings'
 import { useTaskDetailStore } from '@/store/task-detail-store'
 import { useCommandContext } from '@/hooks/use-command-context'
@@ -128,13 +128,17 @@ export function WeekView() {
       let areaId: string | undefined
 
       if (task.project) {
-        const project = projects.find(p => task.project?.includes(p.title))
+        const project = projects.find(p =>
+          matchesWikilinkTitle(task.project, p.title)
+        )
         if (project) {
           projectName = project.title
           projectId = project.id
           // Get area from project if not directly set on task
           if (project.area) {
-            const area = areas.find(a => project.area?.includes(a.title))
+            const area = areas.find(a =>
+              matchesWikilinkTitle(project.area, a.title)
+            )
             if (area) {
               areaName = area.title
               areaId = area.id
@@ -145,7 +149,7 @@ export function WeekView() {
 
       // Direct area on task overrides project's area
       if (task.area) {
-        const area = areas.find(a => task.area?.includes(a.title))
+        const area = areas.find(a => matchesWikilinkTitle(task.area, a.title))
         if (area) {
           areaName = area.title
           areaId = area.id
diff --git a/tdn-desktop/src/hooks/use-sidebar-order.test.ts b/tdn-desktop/src/hooks/use-sidebar-order.test.ts
index 7ba83f39..ac06aedd 100644
--- a/tdn-desktop/src/hooks/use-sidebar-order.test.ts
+++ b/tdn-desktop/src/hooks/use-sidebar-order.test.ts
@@ -126,15 +126,17 @@ describe('useSidebarOrder', () => {
       expect(result.current.orderedAreas[1]!.id).toBe('area-1')
     })
 
-    it('filters out deleted areas from stored order', () => {
+    it('filters out deleted areas and appends new areas', () => {
       useDisplayOrderStore.setState({
         sidebarAreaOrder: ['area-nonexistent', 'area-1'],
       })
 
       const { result } = renderHook(() => useSidebarOrder())
 
-      expect(result.current.orderedAreas).toHaveLength(1)
+      // area-nonexistent is removed, area-1 keeps its position, area-2 is appended
+      expect(result.current.orderedAreas).toHaveLength(2)
       expect(result.current.orderedAreas[0]!.id).toBe('area-1')
+      expect(result.current.orderedAreas[1]!.id).toBe('area-2')
     })
 
     it('excludes archived areas', () => {
@@ -190,7 +192,7 @@ describe('useSidebarOrder', () => {
       expect(projects.map(p => p.id)).toEqual(['project-2', 'project-1'])
     })
 
-    it('filters out deleted projects', () => {
+    it('filters out deleted projects and appends new projects', () => {
       useDisplayOrderStore.setState({
         sidebarProjectOrder: {
           'area-1': ['project-nonexistent', 'project-1'],
@@ -200,7 +202,8 @@ describe('useSidebarOrder', () => {
       const { result } = renderHook(() => useSidebarOrder())
 
       const projects = result.current.getOrderedProjects('area-1')
-      expect(projects.map(p => p.id)).toEqual(['project-1'])
+      // project-nonexistent is removed, project-1 keeps position, project-2 is appended
+      expect(projects.map(p => p.id)).toEqual(['project-1', 'project-2'])
     })
   })
 
diff --git a/tdn-desktop/src/hooks/use-sidebar-order.ts b/tdn-desktop/src/hooks/use-sidebar-order.ts
index 86991a0a..a168eea4 100644
--- a/tdn-desktop/src/hooks/use-sidebar-order.ts
+++ b/tdn-desktop/src/hooks/use-sidebar-order.ts
@@ -6,6 +6,7 @@ import {
   useUpdateProject,
 } from '@/services/vault'
 import { useDisplayOrderStore } from '@/store/display-order-store'
+import { matchesWikilinkTitle } from '@/lib/wikilink'
 import type { SidebarOrder } from '@/types/sidebar-order'
 import { ORPHAN_CONTAINER_ID } from '@/types/sidebar-order'
 
@@ -41,8 +42,14 @@ export function useSidebarOrder() {
   // Compute effective area order
   const effectiveAreaOrder = useMemo(() => {
     if (sidebarAreaOrder) {
-      // Filter to only include IDs that still exist in data
-      return sidebarAreaOrder.filter(id => activeAreas.some(a => a.id === id))
+      // Keep stored order (minus deleted), then append any new items at the end
+      const kept = sidebarAreaOrder.filter(id =>
+        activeAreas.some(a => a.id === id)
+      )
+      const newIds = activeAreas
+        .filter(a => !sidebarAreaOrder.includes(a.id))
+        .map(a => a.id)
+      return [...kept, ...newIds]
     }
     return activeAreas.map(a => a.id)
   }, [sidebarAreaOrder, activeAreas])
@@ -50,21 +57,27 @@ export function useSidebarOrder() {
   // Compute effective project order for a container
   const getEffectiveProjectOrder = useCallback(
     (containerId: string): string[] => {
+      // Get the natural order for this container (used as fallback and for new items)
+      const naturalOrder = (() => {
+        if (containerId === ORPHAN_CONTAINER_ID) {
+          return projects.filter(p => !p.area).map(p => p.id)
+        }
+        const area = areas.find(a => a.id === containerId)
+        if (!area) return []
+        return projects
+          .filter(p => matchesWikilinkTitle(p.area, area.title))
+          .map(p => p.id)
+      })()
+
       if (sidebarProjectOrder?.[containerId]) {
-        // Filter to only include IDs that still exist
-        return sidebarProjectOrder[containerId].filter(id =>
-          projects.some(p => p.id === id)
-        )
+        // Keep stored order (minus deleted), then append any new items at the end
+        const storedOrder = sidebarProjectOrder[containerId]
+        const kept = storedOrder.filter(id => naturalOrder.includes(id))
+        const newIds = naturalOrder.filter(id => !storedOrder.includes(id))
+        return [...kept, ...newIds]
       }
-      // Default: projects in natural order
-      if (containerId === ORPHAN_CONTAINER_ID) {
-        return projects.filter(p => !p.area).map(p => p.id)
-      }
-      // Find area by ID to get its title for wikilink matching
-      // Project.area is a wikilink like "[[Finance]]", not an ID
-      const area = areas.find(a => a.id === containerId)
-      if (!area) return []
-      return projects.filter(p => p.area?.includes(area.title)).map(p => p.id)
+
+      return naturalOrder
     },
     [sidebarProjectOrder, projects, areas]
   )
diff --git a/tdn-desktop/src/lib/wikilink.test.ts b/tdn-desktop/src/lib/wikilink.test.ts
index a679afb5..735657c8 100644
--- a/tdn-desktop/src/lib/wikilink.test.ts
+++ b/tdn-desktop/src/lib/wikilink.test.ts
@@ -3,6 +3,7 @@ import {
   extractWikilinkTitle,
   isWikilink,
   ensureWikilink,
+  matchesWikilinkTitle,
   stripWikilink,
 } from './wikilink'
 
@@ -111,6 +112,32 @@ describe('wikilink', () => {
     })
   })
 
+  describe('matchesWikilinkTitle', () => {
+    it('matches exact wikilink title', () => {
+      expect(matchesWikilinkTitle('[[Work]]', 'Work')).toBe(true)
+      expect(matchesWikilinkTitle('[[My Project]]', 'My Project')).toBe(true)
+    })
+
+    it('matches wikilinks with alias or heading', () => {
+      expect(matchesWikilinkTitle('[[Work|My Job]]', 'Work')).toBe(true)
+      expect(matchesWikilinkTitle('[[Work#Section]]', 'Work')).toBe(true)
+    })
+
+    it('rejects substring matches', () => {
+      expect(matchesWikilinkTitle('[[Homework]]', 'Work')).toBe(false)
+      expect(matchesWikilinkTitle('[[Networking]]', 'Net')).toBe(false)
+    })
+
+    it('handles null and undefined', () => {
+      expect(matchesWikilinkTitle(null, 'Work')).toBe(false)
+      expect(matchesWikilinkTitle(undefined, 'Work')).toBe(false)
+    })
+
+    it('returns false for non-wikilinks', () => {
+      expect(matchesWikilinkTitle('Work', 'Work')).toBe(false)
+    })
+  })
+
   describe('stripWikilink', () => {
     it('extracts title from wikilink', () => {
       expect(stripWikilink('[[Work]]')).toBe('Work')
diff --git a/tdn-desktop/src/lib/wikilink.ts b/tdn-desktop/src/lib/wikilink.ts
index dd43ef44..785588d2 100644
--- a/tdn-desktop/src/lib/wikilink.ts
+++ b/tdn-desktop/src/lib/wikilink.ts
@@ -56,6 +56,27 @@ export function ensureWikilink(value: string): string {
   return isWikilink(trimmed) ? trimmed : `[[${trimmed}]]`
 }
 
+/**
+ * Check if a wikilink reference matches a given title.
+ * Extracts the title from the wikilink and compares it exactly.
+ *
+ * This avoids false positives from substring matching — e.g.,
+ * matchesWikilinkTitle('[[Homework]]', 'Work') returns false.
+ *
+ * @example
+ * matchesWikilinkTitle('[[Work]]', 'Work') // true
+ * matchesWikilinkTitle('[[Work|My Job]]', 'Work') // true
+ * matchesWikilinkTitle('[[Homework]]', 'Work') // false
+ * matchesWikilinkTitle(null, 'Work') // false
+ */
+export function matchesWikilinkTitle(
+  reference: string | null | undefined,
+  title: string
+): boolean {
+  if (!reference) return false
+  return extractWikilinkTitle(reference) === title
+}
+
 /**
  * Strip wikilink brackets from a value if present.
  * Returns the title if it's a wikilink, otherwise returns the trimmed input.
diff --git a/tdn-desktop/src/services/vault/queries.ts b/tdn-desktop/src/services/vault/queries.ts
index 640c4524..dd01e537 100644
--- a/tdn-desktop/src/services/vault/queries.ts
+++ b/tdn-desktop/src/services/vault/queries.ts
@@ -5,6 +5,7 @@
 import { useQuery } from '@tanstack/react-query'
 import { logger } from '@/lib/logger'
 import { filterActiveAreas, filterActiveProjects } from '@/lib/entity-filters'
+import { matchesWikilinkTitle } from '@/lib/wikilink'
 import {
   commands,
   type Task,
@@ -181,11 +182,10 @@ export function useVaultHelpers() {
 
     // Relationship helpers
     // Note: Wikilinks use TITLES (e.g., "[[Finance]]"), not hash IDs.
-    // To match, look up the entity by ID, then use its title in includes().
     getProjectsByAreaId: (areaId: string) => {
       const area = areasById.get(areaId)
       if (!area) return []
-      return projects.filter(p => p.area?.includes(area.title))
+      return projects.filter(p => matchesWikilinkTitle(p.area, area.title))
     },
 
     getOrphanProjects: () => projects.filter(p => !p.area),
@@ -193,13 +193,15 @@ export function useVaultHelpers() {
     getTasksByProjectId: (projectId: string) => {
       const project = projectsById.get(projectId)
       if (!project) return []
-      return tasks.filter(t => t.project?.includes(project.title))
+      return tasks.filter(t => matchesWikilinkTitle(t.project, project.title))
     },
 
     getAreaDirectTasks: (areaId: string) => {
       const area = areasById.get(areaId)
       if (!area) return []
-      return tasks.filter(t => t.area?.includes(area.title) && !t.project)
+      return tasks.filter(
+        t => matchesWikilinkTitle(t.area, area.title) && !t.project
+      )
     },
 
     getOrphanTasks: () => tasks.filter(t => !t.project && !t.area),
@@ -212,7 +214,9 @@ export function useVaultHelpers() {
     getProjectCompletion: (projectId: string) => {
       const project = projectsById.get(projectId)
       if (!project) return 0
-      const projectTasks = tasks.filter(t => t.project?.includes(project.title))
+      const projectTasks = tasks.filter(t =>
+        matchesWikilinkTitle(t.project, project.title)
+      )
       if (projectTasks.length === 0) return 0
 
       const completedCount = projectTasks.filter(
@@ -225,7 +229,9 @@ export function useVaultHelpers() {
     getTaskCounts: (projectId: string) => {
       const project = projectsById.get(projectId)
       if (!project) return { taskCount: 0, completedTaskCount: 0 }
-      const projectTasks = tasks.filter(t => t.project?.includes(project.title))
+      const projectTasks = tasks.filter(t =>
+        matchesWikilinkTitle(t.project, project.title)
+      )
       const completedCount = projectTasks.filter(
         t => t.status === 'done' || t.status === 'dropped'
       ).length