Mem-search enhancements: table output, simplified API, Sonnet default, and removed fake URIs (#317)

* feat: Add batch fetching for observations and update documentation

- Implemented a new endpoint for fetching multiple observations by IDs in a single request.
- Updated the DataRoutes to include a POST /api/observations/batch endpoint.
- Enhanced SKILL.md documentation to reflect changes in the search process and batch fetching capabilities.
- Increased the default limit for search results from 5 to 40 for better usability.

* feat!: Fix timeline parameter passing with SearchManager alignment

BREAKING CHANGE: Timeline MCP tools now use standardized parameter names
- anchor_id → anchor
- before → depth_before
- after → depth_after
- obs_type → type (timeline tool only)

Fixes timeline endpoint failures caused by parameter name mismatch between
MCP layer and SearchManager. Adds new SessionStore methods for fetching
prompts and session summaries by ID.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* docs: reframe timeline parameter fix as bug fix, not breaking change

The timeline tools were completely broken due to parameter name mismatch.
There's nothing to migrate from since the old parameters never worked.

Co-authored-by: Alex Newman <thedotmack@users.noreply.github.com>

* Refactor mem-search documentation and optimize API tool definitions

- Updated SKILL.md to emphasize batch fetching for observations, clarifying usage and efficiency.
- Removed deprecated tools from mcp-server.ts and streamlined tool definitions for clarity.
- Enhanced formatting in FormattingService.ts for better output readability.
- Adjusted SearchManager.ts to improve result headers and removed unnecessary search tips from combined text.

* Refactor FormattingService and SearchManager for table-based output

- Updated FormattingService to format search results as tables, including methods for formatting observations, sessions, and user prompts.
- Removed JSON format handling from SearchManager and streamlined result formatting to consistently use table format.
- Enhanced readability and consistency in search tips and formatting logic.
- Introduced token estimation for observations and improved time formatting.

* refactor: update documentation and API references for version bump and search functionalities

* Refactor code structure for improved readability and maintainability

* chore: change default model from haiku to sonnet

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* feat: unify timeline formatting across search and context services

Extract shared timeline formatting utilities into reusable module to align
MCP search output format with context-generator's date/file-grouped format.

Changes:
- Create src/shared/timeline-formatting.ts with reusable utilities
  (parseJsonArray, formatDateTime, formatTime, formatDate, toRelativePath,
  extractFirstFile, groupByDate)
- Refactor context-generator.ts to use shared utilities
- Update SearchManager.search() to use date/file grouping
- Add search-specific row formatters to FormattingService
- Fix timeline methods to extract actual file paths from metadata
  instead of hardcoding 'General'
- Remove Work column from search output (kept in context output)

Result: Consistent date/file-grouped markdown formatting across both
systems while maintaining their different column requirements.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: remove redundant legend from search output

Remove legend from search/timeline results since it's already shown
in SessionStart context. Saves ~30 tokens per search result.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* Refactor session summary rendering to remove links

- Removed link generation for session summaries in context generation and search manager.
- Updated output formatting to exclude links while maintaining the session summary structure.
- Adjusted related components in TimelineService to ensure consistency across the application.

* fix: move skillPath declaration outside try block to fix scoping bug

The skillPath variable was declared inside the try block but referenced
in the catch block for error logging. Since const is block-scoped, this
would cause a ReferenceError when the error handler executes.

Moved skillPath declaration before the try block so it's accessible in
both try and catch scopes.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* fix: address PR #317 code review feedback

**Critical Fixes:**
- Replace happy_path_error__with_fallback debug calls with proper logger methods in mcp-server.ts
- All HTTP API calls now use logger.debug/error for consistent logging

**Code Quality Improvements:**
- Extract 90-day recency window magic numbers to named constants
- Added RECENCY_WINDOW_DAYS and RECENCY_WINDOW_MS constants in SearchManager

**Documentation:**
- Document model cost implications of Haiku → Sonnet upgrade in CHANGELOG
- Provide clear migration path for users who want to revert to Haiku

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: simplify CHANGELOG - remove cost documentation

Removed model cost comparison documentation per user feedback.
Kept only the technical code quality improvements.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
Co-authored-by: claude[bot] <41898282+claude[bot]@users.noreply.github.com>
Co-authored-by: Alex Newman <thedotmack@users.noreply.github.com>

docs/public/architecture/hooks.mdx

@@ -864,7 +864,7 @@ async startSession(session: ActiveSession, worker?: any) {
   const queryResult = query({
     prompt: messageGenerator,
     options: {
-      model: 'claude-haiku-4-5',
+      model: 'claude-sonnet-4-5',
       disallowedTools: ['Bash', 'Read', 'Write', ...],  // Observer-only
       abortController: session.abortController
     }

docs/public/configuration.mdx

@@ -13,7 +13,7 @@ Settings are managed in `~/.claude-mem/settings.json`. The file is auto-created
 
 | Setting                       | Default                         | Description                           |
 |-------------------------------|---------------------------------|---------------------------------------|
-| `CLAUDE_MEM_MODEL`            | `haiku`                         | AI model for processing observations  |
+| `CLAUDE_MEM_MODEL`            | `sonnet`                        | AI model for processing observations  |
 | `CLAUDE_MEM_CONTEXT_OBSERVATIONS` | `50`                        | Number of observations to inject      |
 | `CLAUDE_MEM_WORKER_PORT`      | `37777`                         | Worker service port                   |
 | `CLAUDE_MEM_SKIP_TOOLS`       | `ListMcpResourcesTool,SlashCommand,Skill,TodoWrite,AskUserQuestion` | Comma-separated tools to exclude from observations |
@@ -35,8 +35,8 @@ Configure which AI model processes your observations.
 
 Shorthand model names automatically forward to the latest version:
 
-- `haiku` - Fast, cost-efficient (default)
-- `sonnet` - Balanced
+- `haiku` - Fast, cost-efficient
+- `sonnet` - Balanced (default)
 - `opus` - Most capable
 
 ### Using the Interactive Script
@@ -53,7 +53,7 @@ Edit `~/.claude-mem/settings.json`:
 
 ```json
 {
-  "CLAUDE_MEM_MODEL": "haiku"
+  "CLAUDE_MEM_MODEL": "sonnet"
 }
 ```
 
@@ -262,7 +262,7 @@ Token economics help you understand the value of cached observations vs. re-read
 
 | Setting | Default | Description |
 |---------|---------|-------------|
-| **Model** | haiku | AI model for generating observations |
+| **Model** | sonnet | AI model for generating observations |
 | **Worker Port** | 37777 | Port for background worker service |
 | **MCP search server** | true | Enable Model Context Protocol search tools |
 | **Include last summary** | false | Add previous session's summary to context |
@@ -420,7 +420,7 @@ npm run worker:logs
 
 ### Invalid Model Name
 
-If you specify an invalid model name, the worker will fall back to `haiku` and log a warning.
+If you specify an invalid model name, the worker will fall back to `sonnet` and log a warning.
 
 Valid shorthand models (forward to latest version):
 - haiku

docs/public/introduction.mdx

@@ -29,7 +29,7 @@ Restart Claude Code. Context from previous sessions will automatically appear in
 - ⚙️ **Context Configuration** - Fine-grained control over what context gets injected
 - 🤖 **Automatic Operation** - No manual intervention required
 - 📊 **FTS5 Search** - Fast full-text search across observations
-- 🔗 **Citations** - Reference past decisions with `claude-mem://` URIs
+- 🔗 **Citations** - Reference past observations with IDs (access via http://localhost:37777/api/observation/{id} or view all in the web viewer at http://localhost:37777)
 
 ## How It Works
 

docs/public/platform-integration.mdx

@@ -46,7 +46,7 @@ GET /api/context/recent?project=my-project&limit=3
 ### Environment Variables
 
 ```bash
-CLAUDE_MEM_MODEL=claude-haiku-4-5           # Model for observations/summaries
+CLAUDE_MEM_MODEL=claude-sonnet-4-5          # Model for observations/summaries
 CLAUDE_MEM_CONTEXT_OBSERVATIONS=50          # Observations injected at SessionStart
 CLAUDE_MEM_WORKER_PORT=37777                # Worker service port
 CLAUDE_MEM_PYTHON_VERSION=3.13              # Python version for chroma-mcp

docs/public/usage/search-tools.mdx

@@ -246,11 +246,10 @@ authentication for better scalability and stateless design...
 
 ## Citations
 
-All search results include citations using the `claude-mem://` URI scheme:
+All search results include observation IDs that can be accessed via the HTTP API:
 
-- `claude-mem://observation/123` - Specific observation
-- `claude-mem://session/abc-456` - Specific session
-- `claude-mem://user-prompt/789` - Specific user prompt
+- `http://localhost:37777/api/observation/{id}` - Get specific observation by ID
+- View all observations in the web viewer at `http://localhost:37777`
 
 These citations enable referencing specific historical context in your work.