memorix 1.1.7 → 1.1.9

package/docs/AGENT_OPERATOR_PLAYBOOK.md

@@ -612,6 +612,7 @@ memorix serve
 memorix background start
 memorix serve-http --port 3211
 memorix doctor
+memorix doctor agents --agent <agent>
 memorix status
 ```
 
@@ -620,6 +621,7 @@ memorix status
 ```bash
 memorix init --global
 memorix setup --agent <agent> --global
+memorix repair agents --agent <agent>
 memorix integrate --agent <agent>
 memorix hooks install --agent <agent>
 memorix git-hook --force
@@ -645,6 +647,22 @@ Use MCP tools:
 
 If Memorix "doesn't work", check these in order.
 
+### 0. Is the agent integration stale?
+
+Run:
+
+```bash
+memorix doctor agents --agent <agent>
+```
+
+If it reports stale MCP command paths, missing `memorix` MCP entries, missing Claude `alwaysLoad`, or outdated Memory Autopilot guidance, run:
+
+```bash
+memorix repair agents --agent <agent>
+```
+
+Repair only rewrites Memorix-owned MCP entries and Memorix-owned guidance blocks. It should not edit unrelated user config.
+
 ### 1. Is the workspace a Git repo?
 
 If not, run:

package/docs/API_REFERENCE.md

@@ -103,6 +103,8 @@ MCP:
 
 `memorix context` defaults to `--refresh auto`, so first use can seed CodeGraph Memory without a separate manual `memorix codegraph refresh`. Its brief puts live package/changelog/Git facts before memory hints and flags old `progress.txt` / dev-log notes as historical when they predate the latest changelog, so agents should treat current facts as the source of truth when files disagree. Task lenses keep the packet shaped to the work: bugfix briefs prefer failing tests and repros, release briefs prefer metadata/changelog/package checks, and onboarding briefs prefer docs and entry points while hiding unrelated suspect details. Use `--refresh never` for read-only inspection and `--refresh always` when you want to force a fresh scan.
 
+Project-specific generated, vendored, or cache paths can be excluded from CodeGraph Memory with `[codegraph].exclude_patterns` in `memorix.toml` or `~/.memorix/config.toml` (`codegraph.excludePatterns` in legacy YAML). User patterns extend the built-in excludes and are applied to indexing, Project Context suggested reads, and Context Pack suggested reads.
+
 SessionStart hooks keep the default minimal hint lightweight. When memory behavior is configured with `sessionInject=full`, Memorix injects the compact Memory Autopilot brief at session start instead of only listing recent text memories.
 
 The intended loop for agents is: get the project brief when it helps, inspect the suggested current files, use stale or unbound memory only as a lead, store durable outcomes after the work changes the project, and resolve obsolete memories.

package/docs/CONFIGURATION.md

@@ -60,6 +60,9 @@ skip_merge_commits = true
 exclude_patterns = ["*.lock", "dist/**"]
 noise_keywords = ["format", "typo"]
 
+[codegraph]
+exclude_patterns = ["vendor/**", "third_party/**", "generated/**"]
+
 [server]
 transport = "stdio"
 dashboard = true
@@ -197,6 +200,21 @@ Project identity is still resolved from the real `.git` root. A project
 `memorix.toml` is an override file under that root; it does not create or rename
 the Memorix project ID.
 
+### `[codegraph]`
+
+CodeGraph Memory and Project Context path filtering.
+
+Common keys:
+
+- `exclude_patterns = ["vendor/**", "third_party/**", "generated/**"]`
+
+Legacy YAML uses `codegraph.excludePatterns` for the same setting.
+
+These patterns extend Memorix's built-in CodeGraph excludes (`node_modules`,
+build outputs, worktrees, and similar generated directories). Matching paths are
+skipped during CodeGraph indexing and hidden from Project Context / Context Pack
+suggested reads.
+
 ### `[server]`
 
 Server and dashboard behavior.