waypoint-codex 0.11.0 → 0.12.1

package/README.md

@@ -55,7 +55,7 @@ That keeps the default conversation focused on diagnosis, progress, and verifica
 Waypoint scaffolds a Codex-friendly repo around a few core pieces:
 
 - `AGENTS.md` for the startup contract
-- `MEMORY.md` for durable user/team preferences and collaboration context
+- `.waypoint/MEMORY.md` for durable user/team preferences and collaboration context
 - `.waypoint/WORKSPACE.md` for live operational state
 - `.waypoint/docs/` for durable project memory
 - `.waypoint/DOCS_INDEX.md` for docs routing
@@ -97,7 +97,6 @@ That gives you a repo that looks roughly like this:
 ```text
 repo/
 ├── AGENTS.md
-├── MEMORY.md
 ├── .codex/
 │   ├── agents/
 │   └── config.toml
@@ -105,6 +104,7 @@ repo/
 │   └── skills/
 └── .waypoint/
     ├── DOCS_INDEX.md
+    ├── MEMORY.md
     ├── TRACKS_INDEX.md
     ├── WORKSPACE.md
     ├── docs/

package/dist/src/core.js

@@ -7,6 +7,7 @@ import { readTemplate, renderWaypointConfig, MANAGED_BLOCK_END, MANAGED_BLOCK_ST
 const DEFAULT_CONFIG_PATH = ".waypoint/config.toml";
 const DEFAULT_DOCS_DIR = ".waypoint/docs";
 const DEFAULT_DOCS_INDEX = ".waypoint/DOCS_INDEX.md";
+const DEFAULT_MEMORY = ".waypoint/MEMORY.md";
 const DEFAULT_TRACK_DIR = ".waypoint/track";
 const DEFAULT_TRACKS_INDEX = ".waypoint/TRACKS_INDEX.md";
 const DEFAULT_WORKSPACE = ".waypoint/WORKSPACE.md";
@@ -37,11 +38,20 @@ const LEGACY_WAYPOINT_GITIGNORE_RULES = new Set([
     ".agents/skills/workspace-compress/",
     ".agents/skills/pre-pr-hygiene/",
     ".agents/skills/pr-review/",
+    ".waypoint/config.toml",
+    ".waypoint/README.md",
+    ".waypoint/SOUL.md",
+    ".waypoint/WORKSPACE.md",
+    ".waypoint/agent-operating-manual.md",
     ".waypoint/",
     ".waypoint/DOCS_INDEX.md",
+    ".waypoint/TRACKS_INDEX.md",
     ".waypoint/state/",
     ".waypoint/context/",
+    ".waypoint/scripts/",
+    ".waypoint/track/",
     ".waypoint/*",
+    "!.waypoint/MEMORY.md",
     "!.waypoint/docs/",
     "!.waypoint/docs/**",
     ".waypoint/docs/README.md",
@@ -97,7 +107,13 @@ function migrateLegacyRootFiles(projectRoot) {
     if (existsSync(legacyWorkspace) && !existsSync(newWorkspace)) {
         writeText(newWorkspace, readFileSync(legacyWorkspace, "utf8"));
     }
+    const legacyMemory = path.join(projectRoot, "MEMORY.md");
+    const newMemory = path.join(projectRoot, DEFAULT_MEMORY);
+    if (existsSync(legacyMemory) && !existsSync(newMemory)) {
+        writeText(newMemory, readFileSync(legacyMemory, "utf8"));
+    }
     removePathIfExists(legacyWorkspace);
+    removePathIfExists(legacyMemory);
     removePathIfExists(path.join(projectRoot, "DOCS_INDEX.md"));
 }
 function appendGitignoreSnippet(projectRoot) {
@@ -293,7 +309,7 @@ export function initRepository(projectRoot, options) {
     writeText(path.join(projectRoot, ".waypoint/README.md"), readTemplate(".waypoint/README.md"));
     writeText(path.join(projectRoot, ".waypoint/SOUL.md"), readTemplate(".waypoint/SOUL.md"));
     writeText(path.join(projectRoot, ".waypoint/agent-operating-manual.md"), readTemplate(".waypoint/agent-operating-manual.md"));
-    writeIfMissing(path.join(projectRoot, "MEMORY.md"), readTemplate("MEMORY.md"));
+    writeIfMissing(path.join(projectRoot, DEFAULT_MEMORY), readTemplate(".waypoint/MEMORY.md"));
     scaffoldWaypointOptionalTemplates(projectRoot);
     writeText(path.join(projectRoot, DEFAULT_CONFIG_PATH), renderWaypointConfig({
         profile: options.profile,
@@ -314,7 +330,7 @@ export function initRepository(projectRoot, options) {
     return [
         "Initialized Waypoint scaffold",
         "Installed managed AGENTS block",
-        "Created MEMORY.md, .waypoint/WORKSPACE.md, .waypoint/docs/, and .waypoint/track/ scaffold",
+        "Created .waypoint/MEMORY.md, .waypoint/WORKSPACE.md, .waypoint/docs/, and .waypoint/track/ scaffold",
         "Installed repo-local Waypoint skills",
         "Installed coding/reviewer agents and project Codex config",
         "Generated .waypoint/DOCS_INDEX.md and .waypoint/TRACKS_INDEX.md",
@@ -426,7 +442,7 @@ export function doctorRepository(projectRoot) {
         }
     }
     for (const requiredFile of [
-        path.join(projectRoot, "MEMORY.md"),
+        path.join(projectRoot, DEFAULT_MEMORY),
         path.join(projectRoot, ".waypoint", "SOUL.md"),
         path.join(projectRoot, ".waypoint", "agent-operating-manual.md"),
         path.join(projectRoot, ".waypoint", "scripts", "prepare-context.mjs"),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "waypoint-codex",
-  "version": "0.11.0",
+  "version": "0.12.1",
   "description": "Codex-native repository operating system: scaffolding, docs routing, repo-local skills, doctor, and sync.",
   "license": "MIT",
   "type": "module",

package/templates/.codex/agents/coding-agent.toml

@@ -4,7 +4,7 @@ sandbox_mode = "workspace-write"
 developer_instructions = """
 Read these files in order before doing anything else:
 1. .waypoint/SOUL.md
-2. MEMORY.md if it exists
+2. .waypoint/MEMORY.md if it exists
 3. .waypoint/agent-operating-manual.md
 4. .waypoint/WORKSPACE.md
 5. .waypoint/context/MANIFEST.md

package/templates/.gitignore.snippet

@@ -19,9 +19,17 @@
 .agents/skills/workspace-compress/
 .agents/skills/pre-pr-hygiene/
 .agents/skills/pr-review/
-.waypoint/*
-!.waypoint/docs/
-!.waypoint/docs/**
+.waypoint/config.toml
+.waypoint/README.md
+.waypoint/SOUL.md
+.waypoint/WORKSPACE.md
+.waypoint/agent-operating-manual.md
+.waypoint/DOCS_INDEX.md
+.waypoint/TRACKS_INDEX.md
+.waypoint/context/
+.waypoint/scripts/
+.waypoint/state/
+.waypoint/track/
 .waypoint/docs/README.md
 .waypoint/docs/code-guide.md
 # End Waypoint state

package/templates/.waypoint/README.md

@@ -2,7 +2,7 @@
 
 Repo-local Waypoint configuration and project memory files.
 
-- repo root `MEMORY.md` — durable user/team preferences, collaboration context, and stable product defaults
+- `MEMORY.md` — durable user/team preferences, collaboration context, and stable product defaults
 - `config.toml` — Waypoint feature toggles and file locations
 - `WORKSPACE.md` — live operational state; new or materially revised entries in multi-topic sections are timestamped
 - `DOCS_INDEX.md` — generated docs routing map

package/templates/.waypoint/agent-operating-manual.md

@@ -18,7 +18,7 @@ Bootstrap sequence:
 
 1. Run `node .waypoint/scripts/prepare-context.mjs`
 2. Read `.waypoint/SOUL.md`
-3. Read `MEMORY.md` if it exists
+3. Read `.waypoint/MEMORY.md` if it exists
 4. Read this file
 5. Read `.waypoint/WORKSPACE.md`
 6. Read `.waypoint/context/MANIFEST.md`
@@ -35,7 +35,7 @@ Do not skip this sequence.
 
 The repository should contain the context the next agent needs.
 
-- `MEMORY.md` is the durable user/team memory layer: collaboration preferences, stable defaults, and long-lived context that should survive across sessions
+- `.waypoint/MEMORY.md` is the durable user/team memory layer: collaboration preferences, stable defaults, and long-lived context that should survive across sessions
 - `.waypoint/WORKSPACE.md` is the live operational record: in progress, current state, next steps
 - `.waypoint/track/` is the optional execution-tracking layer for active long-running work that genuinely needs durable progress state
 - `.waypoint/docs/` is the durable project memory: architecture, decisions, integration notes, debugging knowledge, and durable plans
@@ -51,7 +51,7 @@ If something important lives only in your head or in the chat transcript, the re
 - When the user shows a bug, screenshot, or broken behavior, investigate first. Lead with what is happening, why it is likely happening, what you checked, and what you are doing next.
 - Do not lead with readiness disclaimers such as "I can't call this done yet" unless the user explicitly asked whether the work is ready, shippable, or complete.
 - Honesty means accurate diagnosis, explicit uncertainty, and clear verification limits. It does not mean substituting process language for investigation.
-- Update `MEMORY.md` only when you learned a durable user/team preference, collaboration rule, or stable product default.
+- Update `.waypoint/MEMORY.md` only when you learned a durable user/team preference, collaboration rule, or stable product default.
 - Update `.waypoint/WORKSPACE.md` as live execution state when progress meaningfully changes. In multi-topic sections, prefix new or materially revised bullets with a local timestamp like `[2026-03-06 20:10 PST]`.
 - For large multi-step work that is likely to span sessions or needs durable progress state, create or update a tracker in `.waypoint/track/`, keep detailed execution state there, and point at it from `## Active Trackers` in `.waypoint/WORKSPACE.md`.
 - Update `.waypoint/docs/` when durable knowledge changes, and refresh each changed routable doc's `last_updated` field.

package/templates/managed-agents-block.md

@@ -17,7 +17,7 @@ Run the Waypoint bootstrap only in these cases:
 Bootstrap sequence:
 1. Run `node .waypoint/scripts/prepare-context.mjs`
 2. Read `.waypoint/SOUL.md`
-3. Read `MEMORY.md` if it exists
+3. Read `.waypoint/MEMORY.md` if it exists
 4. Read `.waypoint/agent-operating-manual.md`
 5. Read `.waypoint/WORKSPACE.md`
 6. Read `.waypoint/context/MANIFEST.md`
@@ -91,7 +91,7 @@ Delivery expectations:
 
 Working rules:
 - Keep `.waypoint/WORKSPACE.md` current as the live execution state, with timestamped new or materially revised entries in multi-topic sections
-- Keep `MEMORY.md` for durable user/team preferences, collaboration context, and stable product defaults; keep task status and active execution state out of it
+- Keep `.waypoint/MEMORY.md` for durable user/team preferences, collaboration context, and stable product defaults; keep task status and active execution state out of it
 - Update `.waypoint/docs/` when behavior or durable project knowledge changes, and refresh `last_updated` on touched routable docs
 - Keep most work in the main agent. Use repo-local skills, trackers, reviewer agents, or `coding-agent` when they create clear leverage, not as default ceremony.
 - Use `work-tracker` when work is likely to span sessions or needs durable progress tracking.