waypoint-codex 0.20.0 → 1.0.1

package/README.md

@@ -73,7 +73,7 @@ better default.
 ### 1. Better default behavior
 
 Waypoint gives Codex stronger repo guidance through the generated contract,
-operating manual, core behavior files, and repo-local instructions.
+workspace files, and repo-local instructions.
 
 That means the agent is pushed to:
 
@@ -120,9 +120,7 @@ Waypoint also helps Codex follow through on bigger tasks.
 
 It includes workflows for:
 
-- long-running task tracking
 - ship-readiness audits
-- merge-ready ownership
 - deliberate review passes before PR or merge
 
 This helps the agent keep moving until the work is actually ready, not just
@@ -141,8 +139,6 @@ That includes:
 - user-scoped guidance for true cross-project standing rules
 - project-scoped guidance for durable repo-wide context and always-on rules
 - repo-local skills for workflow-specific or method-specific guidance
-- retrospectives that turn friction from the current conversation into lasting
-  improvements
 
 ### 6. Better continuity
 
@@ -163,23 +159,20 @@ Waypoint scaffolds a Codex-friendly repo around a few core pieces:
 
 - `AGENTS.md` for the project-scoped startup contract and durable repo guidance
 - `.waypoint/WORKSPACE.md` for live operational state
-- `.waypoint/ACTIVE_PLANS.md` for the currently approved plan and active phase checkpoints
+- `.waypoint/ACTIVE_PLANS.md` for the current active plan, checklist, blockers, and verification state
 - `.waypoint/docs/` for long-lived project docs
 - `.waypoint/plans/` for durable plan documents
-- `.waypoint/DOCS_INDEX.md` for docs and plans routing, so the agent knows what
-  to read and when
-- `.waypoint/context/` for generated startup context
+- `.waypoint/DOCS_INDEX.md` for docs routing, so the agent knows what to read and when
+- `.waypoint/context/` for generated volatile context
+- `.waypoint/context/SNAPSHOT.md` for repo state and PR context
 - `.waypoint/context/RECENT_THREAD.md` for compact continuity from the previous
   conversation
-- `.waypoint/track/` for long-running work that truly needs durable progress
-  tracking
 - `.agents/skills/` for optional structured workflows
 - `.codex/` for optional reviewer and helper agents
 
-By default, Waypoint routes docs from `.waypoint/docs/` and plans from
-`.waypoint/plans/`.
+By default, Waypoint routes docs from `.waypoint/docs/`.
 If your repo keeps routable docs elsewhere, you can add more explicit roots in
-`.waypoint/config.toml` with `docs_dirs` and `plans_dirs`.
+`.waypoint/config.toml` with `docs_dirs`.
 Waypoint scans each configured root recursively and only includes Markdown files
 with valid Waypoint frontmatter.
 
@@ -237,12 +230,10 @@ repo/
 │   └── skills/
 └── .waypoint/
     ├── DOCS_INDEX.md
-    ├── TRACKS_INDEX.md
     ├── WORKSPACE.md
     ├── ACTIVE_PLANS.md
     ├── docs/
     ├── plans/
-    ├── track/
     ├── context/
     ├── scripts/
     └── ...
@@ -257,11 +248,6 @@ docs_dirs = [
   ".waypoint/docs",
   "services/app/docs",
 ]
-
-plans_dirs = [
-  ".waypoint/plans",
-  "services/app/plans",
-]
 ```
 
 ## Built-in skills
@@ -269,18 +255,13 @@ plans_dirs = [
 Waypoint ships a strong default skill pack for real coding work:
 
 - `planning`
-- `work-tracker`
-- `docs-sync`
 - `code-guide-audit`
 - `adversarial-review`
-- `break-it-qa`
-- `conversation-retrospective`
 - `frontend-ship-audit`
 - `backend-ship-audit`
-- `merge-ready-owner`
-- `workspace-compress`
-- `pre-pr-hygiene`
 - `pr-review`
+- `frontend-context-interview`
+- `backend-context-interview`
 - `agi-help`
 
 These are repo-local, so the workflow travels with the project.
@@ -305,18 +286,18 @@ The most important ones are:
   pass
 - `frontend-ship-audit` when frontend work needs a deeper product, UX, and ship
   readiness pass
-- `docs-sync` when the implementation changed and the repo docs should be
-  brought back in sync
-- `conversation-retrospective` when the conversation exposed friction,
-  corrections, or workflow problems that should become durable improvements
-- `merge-ready-owner` when you want the agent to own the task all the way to a
-  merge-ready result with stronger autonomy
+- `frontend-context-interview` / `backend-context-interview` when durable
+  project context is missing and would materially change implementation choices
+- `pr-review` when an open PR already has active review comments or automated
+  review in flight
+- `agi-help` when you want a high-quality external handoff package for
+  GPT-5.4-Pro
 
 The practical rule is:
 
 - install Waypoint for better defaults
 - invoke the higher-rigor skills when you want a stronger planning, audit,
-  review, docs, or closeout pass
+  review, or closeout pass
 
 ## Reviewer agents
 
@@ -326,7 +307,7 @@ Waypoint scaffolds these reviewer agents by default:
 - `code-reviewer`
 - `plan-reviewer`
 
-They are available for deliberate second passes and for ownership workflows like `merge-ready-owner`.
+They are available for deliberate second passes.
 
 ## What makes Waypoint different
 
@@ -346,7 +327,7 @@ Waypoint is opinionated, but explicit:
 
 - `waypoint init` — scaffold or refresh the repo and, by default, update the global CLI first
 - `waypoint doctor` — validate health and report drift
-- `waypoint sync` — rebuild the docs/plans and tracker indexes
+- `waypoint sync` — rebuild the docs index
 - `waypoint upgrade` — update the CLI and refresh the current repo using its saved config
 
 ## Learn more

package/dist/src/cli.js

@@ -29,7 +29,7 @@ function printHelp() {
 Commands:
   init                Initialize a repository with Waypoint scaffolding (auto-updates CLI unless skipped)
   doctor              Validate repository health and report drift
-  sync                Rebuild docs/plans and tracker indexes
+  sync                Rebuild the docs index
   upgrade             Update the global Waypoint CLI and refresh this repo using existing config
 `);
 }

package/dist/src/core.js

@@ -2,14 +2,11 @@ import { existsSync, mkdirSync, readFileSync, readdirSync, realpathSync, rmSync,
 import path from "node:path";
 import * as TOML from "@iarna/toml";
 import { renderDocsIndex } from "./docs-index.js";
-import { renderTracksIndex } from "./track-index.js";
 import { defaultWaypointConfig, readTemplate, renderWaypointConfig, MANAGED_BLOCK_END, MANAGED_BLOCK_START, templatePath, } from "./templates.js";
 const DEFAULT_CONFIG_PATH = ".waypoint/config.toml";
 const DEFAULT_DOCS_DIR = ".waypoint/docs";
 const DEFAULT_DOCS_INDEX = ".waypoint/DOCS_INDEX.md";
 const DEFAULT_PLANS_DIR = ".waypoint/plans";
-const DEFAULT_TRACK_DIR = ".waypoint/track";
-const DEFAULT_TRACKS_INDEX = ".waypoint/TRACKS_INDEX.md";
 const DEFAULT_WORKSPACE = ".waypoint/WORKSPACE.md";
 const DEFAULT_ACTIVE_PLANS = ".waypoint/ACTIVE_PLANS.md";
 const GITIGNORE_WAYPOINT_START = "# Waypoint state";
@@ -25,34 +22,24 @@ const LEGACY_WAYPOINT_GITIGNORE_RULES = new Set([
     ".agents/",
     ".agents/skills/",
     ".agents/skills/planning/",
-    ".agents/skills/work-tracker/",
-    ".agents/skills/docs-sync/",
     ".agents/skills/code-guide-audit/",
     ".agents/skills/adversarial-review/",
     ".agents/skills/visual-explanations/",
-    ".agents/skills/break-it-qa/",
     ".agents/skills/frontend-context-interview/",
     ".agents/skills/backend-context-interview/",
     ".agents/skills/frontend-ship-audit/",
     ".agents/skills/backend-ship-audit/",
-    ".agents/skills/conversation-retrospective/",
-    ".agents/skills/merge-ready-owner/",
-    ".agents/skills/workspace-compress/",
-    ".agents/skills/pre-pr-hygiene/",
     ".agents/skills/pr-review/",
+    ".agents/skills/agi-help/",
     ".waypoint/config.toml",
     ".waypoint/README.md",
-    ".waypoint/SOUL.md",
     ".waypoint/WORKSPACE.md",
     ".waypoint/ACTIVE_PLANS.md",
-    ".waypoint/agent-operating-manual.md",
     ".waypoint/",
     ".waypoint/DOCS_INDEX.md",
-    ".waypoint/TRACKS_INDEX.md",
     ".waypoint/state/",
     ".waypoint/context/",
     ".waypoint/scripts/",
-    ".waypoint/track/",
     ".waypoint/plans/",
     ".waypoint/*",
     "!.waypoint/docs/",
@@ -62,16 +49,10 @@ const LEGACY_WAYPOINT_GITIGNORE_RULES = new Set([
 ]);
 const SHIPPED_SKILL_NAMES = [
     "planning",
-    "work-tracker",
-    "docs-sync",
     "code-guide-audit",
     "adversarial-review",
-    "break-it-qa",
-    "conversation-retrospective",
-    "merge-ready-owner",
-    "workspace-compress",
-    "pre-pr-hygiene",
     "pr-review",
+    "agi-help",
     "frontend-context-interview",
     "backend-context-interview",
     "frontend-ship-audit",
@@ -79,7 +60,6 @@ const SHIPPED_SKILL_NAMES = [
 ];
 const TIMESTAMPED_WORKSPACE_SECTIONS = new Set([
     "## Active Plans",
-    "## Active Trackers",
     "## Current State",
     "## In Progress",
     "## Next",
@@ -121,25 +101,16 @@ function configuredRootDirs(projectRoot, roots, legacyRoot, fallbackRoot) {
 function docsRootDirs(projectRoot, config) {
     return configuredRootDirs(projectRoot, config?.docs_dirs, config?.docs_dir, DEFAULT_DOCS_DIR);
 }
-function plansRootDirs(projectRoot, config) {
-    return configuredRootDirs(projectRoot, config?.plans_dirs, config?.plans_dir, DEFAULT_PLANS_DIR);
-}
 function docsSectionHeading(projectRoot, dir) {
     const relativePath = path.relative(projectRoot, dir).split(path.sep).join("/");
     const normalizedPath = relativePath.length === 0 ? "." : relativePath;
     return normalizedPath.endsWith("/") ? normalizedPath : `${normalizedPath}/`;
 }
 function docsIndexSections(projectRoot, config) {
-    return [
-        ...docsRootDirs(projectRoot, config).map((dir) => ({
-            heading: docsSectionHeading(projectRoot, dir),
-            dir,
-        })),
-        ...plansRootDirs(projectRoot, config).map((dir) => ({
-            heading: docsSectionHeading(projectRoot, dir),
-            dir,
-        })),
-    ];
+    return docsRootDirs(projectRoot, config).map((dir) => ({
+        heading: docsSectionHeading(projectRoot, dir),
+        dir,
+    }));
 }
 function buildWaypointConfig(projectRoot, existingConfig, options) {
     const defaults = defaultWaypointConfig({ profile: options.profile });
@@ -149,12 +120,7 @@ function buildWaypointConfig(projectRoot, existingConfig, options) {
         coding_agent: existingConfig?.coding_agent ?? defaults.coding_agent,
         workspace_file: existingConfig?.workspace_file ?? defaults.workspace_file,
         docs_dirs: configuredRootDirs(projectRoot, existingConfig?.docs_dirs, existingConfig?.docs_dir, DEFAULT_DOCS_DIR).map((dir) => path.relative(projectRoot, dir).split(path.sep).join("/")),
-        plans_dirs: configuredRootDirs(projectRoot, existingConfig?.plans_dirs, existingConfig?.plans_dir, DEFAULT_PLANS_DIR).map((dir) => path.relative(projectRoot, dir).split(path.sep).join("/")),
         docs_index_file: existingConfig?.docs_index_file ?? defaults.docs_index_file,
-        features: {
-            repo_skills: existingConfig?.features?.repo_skills ?? defaults.features?.repo_skills,
-            docs_index: existingConfig?.features?.docs_index ?? defaults.features?.docs_index,
-        },
     };
 }
 function ensureDir(dirPath) {
@@ -336,7 +302,6 @@ function scaffoldSkills(projectRoot) {
 }
 function scaffoldWaypointOptionalTemplates(projectRoot) {
     copyTemplateTree(templatePath(".waypoint/scripts"), path.join(projectRoot, ".waypoint/scripts"));
-    copyTemplateTree(templatePath(".waypoint/track"), path.join(projectRoot, ".waypoint/track"));
 }
 function scaffoldOptionalCodex(projectRoot) {
     copyTemplateTree(templatePath(".codex"), path.join(projectRoot, ".codex"));
@@ -367,6 +332,13 @@ export function initRepository(projectRoot, options) {
         ".agents/skills/waypoint-explore",
         ".agents/skills/waypoint-research",
         ".agents/skills/visual-explanations",
+        ".agents/skills/work-tracker",
+        ".agents/skills/docs-sync",
+        ".agents/skills/break-it-qa",
+        ".agents/skills/conversation-retrospective",
+        ".agents/skills/merge-ready-owner",
+        ".agents/skills/workspace-compress",
+        ".agents/skills/pre-pr-hygiene",
         ".codex/agents/explorer.toml",
         ".codex/agents/reviewer.toml",
         ".codex/agents/architect.toml",
@@ -376,19 +348,27 @@ export function initRepository(projectRoot, options) {
         ".waypoint/MEMORY.md",
         ".waypoint/rules",
         ".waypoint/state",
+        ".waypoint/SOUL.md",
+        ".waypoint/agent-operating-manual.md",
+        ".waypoint/TRACKS_INDEX.md",
+        ".waypoint/track",
+        ".waypoint/context/MANIFEST.md",
+        ".waypoint/context/ACTIVE_PLANS.md",
+        ".waypoint/context/ACTIVE_TRACKERS.md",
+        ".waypoint/context/PULL_REQUESTS.md",
+        ".waypoint/context/RECENT_COMMITS.md",
+        ".waypoint/context/UNCOMMITTED_CHANGES.md",
+        ".waypoint/scripts/build-track-index.mjs",
     ]) {
         removePathIfExists(path.join(projectRoot, deprecatedPath));
     }
     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"));
     scaffoldWaypointOptionalTemplates(projectRoot);
     writeText(path.join(projectRoot, DEFAULT_CONFIG_PATH), renderWaypointConfig(config));
     writeIfMissing(path.join(projectRoot, DEFAULT_WORKSPACE), readTemplate("WORKSPACE.md"));
     writeIfMissing(path.join(projectRoot, DEFAULT_ACTIVE_PLANS), readTemplate(".waypoint/ACTIVE_PLANS.md"));
     ensureDir(path.join(projectRoot, DEFAULT_DOCS_DIR));
     ensureDir(path.join(projectRoot, DEFAULT_PLANS_DIR));
-    ensureDir(path.join(projectRoot, DEFAULT_TRACK_DIR));
     writeIfMissing(path.join(projectRoot, ".waypoint/docs/README.md"), readTemplate(".waypoint/docs/README.md"));
     writeIfMissing(path.join(projectRoot, ".waypoint/docs/code-guide.md"), readTemplate(".waypoint/docs/code-guide.md"));
     writeIfMissing(path.join(projectRoot, ".waypoint/plans/README.md"), readTemplate(".waypoint/plans/README.md"));
@@ -398,16 +378,14 @@ export function initRepository(projectRoot, options) {
     appendGitignoreSnippet(projectRoot);
     const docsIndexPath = path.join(projectRoot, config.docs_index_file ?? DEFAULT_DOCS_INDEX);
     const docsIndex = renderDocsIndex(projectRoot, docsIndexSections(projectRoot, config));
-    const tracksIndex = renderTracksIndex(projectRoot, path.join(projectRoot, DEFAULT_TRACK_DIR));
     writeText(docsIndexPath, `${docsIndex.content}\n`);
-    writeText(path.join(projectRoot, DEFAULT_TRACKS_INDEX), `${tracksIndex.content}\n`);
     return [
         "Initialized Waypoint scaffold",
         "Installed managed AGENTS block",
-        "Created .waypoint/WORKSPACE.md, .waypoint/ACTIVE_PLANS.md, .waypoint/docs/, .waypoint/plans/, and .waypoint/track/ scaffold",
+        "Created .waypoint/WORKSPACE.md, .waypoint/ACTIVE_PLANS.md, .waypoint/docs/, and .waypoint/plans/ scaffold",
         "Installed repo-local Waypoint skills",
         "Installed coding/reviewer agents and project Codex config",
-        "Generated .waypoint/DOCS_INDEX.md and .waypoint/TRACKS_INDEX.md",
+        "Generated .waypoint/DOCS_INDEX.md",
     ];
 }
 export function loadWaypointConfig(projectRoot) {
@@ -488,7 +466,6 @@ export function doctorRepository(projectRoot) {
         for (const section of [
             "## Active Goal",
             "## Active Plans",
-            "## Active Trackers",
             "## Current State",
             "## In Progress",
             "## Next",
@@ -517,11 +494,8 @@ export function doctorRepository(projectRoot) {
         }
     }
     for (const requiredFile of [
-        path.join(projectRoot, ".waypoint", "SOUL.md"),
-        path.join(projectRoot, ".waypoint", "agent-operating-manual.md"),
         path.join(projectRoot, ".waypoint", "scripts", "prepare-context.mjs"),
         path.join(projectRoot, ".waypoint", "scripts", "build-docs-index.mjs"),
-        path.join(projectRoot, ".waypoint", "scripts", "build-track-index.mjs"),
     ]) {
         if (!existsSync(requiredFile)) {
             findings.push({
@@ -535,11 +509,7 @@ export function doctorRepository(projectRoot) {
     }
     const docsIndexPath = path.join(projectRoot, config.docs_index_file ?? DEFAULT_DOCS_INDEX);
     const configuredDocsDirs = docsRootDirs(projectRoot, config);
-    const configuredPlansDirs = plansRootDirs(projectRoot, config);
     const docsIndex = renderDocsIndex(projectRoot, docsIndexSections(projectRoot, config));
-    const trackDir = path.join(projectRoot, DEFAULT_TRACK_DIR);
-    const tracksIndexPath = path.join(projectRoot, DEFAULT_TRACKS_INDEX);
-    const tracksIndex = renderTracksIndex(projectRoot, trackDir);
     for (const docsDir of configuredDocsDirs) {
         if (existsSync(docsDir)) {
             continue;
@@ -552,15 +522,13 @@ export function doctorRepository(projectRoot) {
             paths: [docsDir],
         });
     }
-    for (const plansDir of configuredPlansDirs) {
-        if (existsSync(plansDir)) {
-            continue;
-        }
+    const plansDir = path.join(projectRoot, DEFAULT_PLANS_DIR);
+    if (!existsSync(plansDir)) {
         findings.push({
             severity: "error",
             category: "docs",
-            message: `${docsSectionHeading(projectRoot, plansDir)} directory is missing.`,
-            remediation: "Create the configured plans directory or update `.waypoint/config.toml`.",
+            message: ".waypoint/plans/ directory is missing.",
+            remediation: "Run `waypoint init` to restore the plans directory.",
             paths: [plansDir],
         });
     }
@@ -578,7 +546,7 @@ export function doctorRepository(projectRoot) {
             severity: "warn",
             category: "docs",
             message: ".waypoint/DOCS_INDEX.md is missing.",
-            remediation: "Run `waypoint sync` to generate the docs/plans index.",
+            remediation: "Run `waypoint sync` to generate the docs index.",
             paths: [docsIndexPath],
         });
     }
@@ -587,46 +555,10 @@ export function doctorRepository(projectRoot) {
             severity: "warn",
             category: "docs",
             message: ".waypoint/DOCS_INDEX.md is stale.",
-            remediation: "Run `waypoint sync` to rebuild the docs/plans index.",
+            remediation: "Run `waypoint sync` to rebuild the docs index.",
             paths: [docsIndexPath],
         });
     }
-    if (!existsSync(trackDir)) {
-        findings.push({
-            severity: "error",
-            category: "track",
-            message: ".waypoint/track/ directory is missing.",
-            remediation: "Run `waypoint init` to scaffold track files.",
-            paths: [trackDir],
-        });
-    }
-    for (const relPath of tracksIndex.invalidTracks) {
-        findings.push({
-            severity: "warn",
-            category: "track",
-            message: `Tracker is missing valid frontmatter or status: ${relPath}`,
-            remediation: "Add `summary`, `last_updated`, `status`, and `read_when` frontmatter using the track template.",
-            paths: [path.join(projectRoot, relPath)],
-        });
-    }
-    if (!existsSync(tracksIndexPath)) {
-        findings.push({
-            severity: "warn",
-            category: "track",
-            message: ".waypoint/TRACKS_INDEX.md is missing.",
-            remediation: "Run `waypoint sync` to generate the tracks index.",
-            paths: [tracksIndexPath],
-        });
-    }
-    else if (readFileSync(tracksIndexPath, "utf8").trimEnd() !== tracksIndex.content.trimEnd()) {
-        findings.push({
-            severity: "warn",
-            category: "track",
-            message: ".waypoint/TRACKS_INDEX.md is stale.",
-            remediation: "Run `waypoint sync` to rebuild the tracks index.",
-            paths: [tracksIndexPath],
-        });
-    }
     const activePlansPath = path.join(projectRoot, DEFAULT_ACTIVE_PLANS);
     if (!existsSync(activePlansPath)) {
         findings.push({
@@ -646,17 +578,6 @@ export function doctorRepository(projectRoot) {
             paths: [workspacePath, activePlansPath],
         });
     }
-    if (existsSync(workspacePath) &&
-        tracksIndex.activeTrackPaths.length > 0 &&
-        !tracksIndex.activeTrackPaths.some((trackPath) => readFileSync(workspacePath, "utf8").includes(trackPath))) {
-        findings.push({
-            severity: "warn",
-            category: "track",
-            message: "Workspace does not reference any active tracker file.",
-            remediation: "Add the active `.waypoint/track/*.md` file paths under `## Active Trackers` in `.waypoint/WORKSPACE.md`.",
-            paths: [workspacePath, ...tracksIndex.activeTrackPaths.map((trackPath) => path.join(projectRoot, trackPath))],
-        });
-    }
     for (const skillName of SHIPPED_SKILL_NAMES) {
         const skillPath = path.join(projectRoot, ".agents/skills", skillName, "SKILL.md");
         if (!existsSync(skillPath)) {
@@ -696,10 +617,6 @@ export function syncRepository(projectRoot) {
     const config = loadWaypointConfig(projectRoot);
     const docsIndexPath = path.join(projectRoot, config.docs_index_file ?? DEFAULT_DOCS_INDEX);
     const docsIndex = renderDocsIndex(projectRoot, docsIndexSections(projectRoot, config));
-    const trackDir = path.join(projectRoot, DEFAULT_TRACK_DIR);
-    const tracksIndexPath = path.join(projectRoot, DEFAULT_TRACKS_INDEX);
-    const tracksIndex = renderTracksIndex(projectRoot, trackDir);
     writeText(docsIndexPath, `${docsIndex.content}\n`);
-    writeText(tracksIndexPath, `${tracksIndex.content}\n`);
-    return ["Rebuilt .waypoint/DOCS_INDEX.md", "Rebuilt .waypoint/TRACKS_INDEX.md"];
+    return ["Rebuilt .waypoint/DOCS_INDEX.md"];
 }

package/dist/src/docs-index.js

@@ -95,7 +95,7 @@ export function renderDocsIndex(projectRoot, sections) {
     const lines = [
         "# Docs Index",
         "",
-        "Auto-generated by `waypoint sync` / `waypoint doctor`. Read matching docs and plans before working on a task.",
+        "Auto-generated by `waypoint sync` / `waypoint doctor`. Read matching docs before working on a task.",
         "",
     ];
     const invalidDocs = [];

package/dist/src/templates.js

@@ -33,12 +33,7 @@ export function defaultWaypointConfig(options) {
         coding_agent: "codex",
         workspace_file: ".waypoint/WORKSPACE.md",
         docs_dirs: [".waypoint/docs"],
-        plans_dirs: [".waypoint/plans"],
         docs_index_file: ".waypoint/DOCS_INDEX.md",
-        features: {
-            repo_skills: true,
-            docs_index: true,
-        },
     };
 }
 export function renderWaypointConfig(config) {
@@ -48,12 +43,7 @@ export function renderWaypointConfig(config) {
         coding_agent: config.coding_agent,
         workspace_file: config.workspace_file,
         docs_dirs: config.docs_dirs,
-        plans_dirs: config.plans_dirs,
         docs_index_file: config.docs_index_file,
-        features: config.features ? {
-            repo_skills: config.features.repo_skills,
-            docs_index: config.features.docs_index,
-        } : undefined,
     };
     return TOML.stringify(renderedConfig);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "waypoint-codex",
-  "version": "0.20.0",
+  "version": "1.0.1",
   "description": "Make Codex better by default with stronger planning, code quality, reviews, tracking, and repo guidance.",
   "license": "MIT",
   "type": "module",

package/templates/.agents/skills/agi-help/SKILL.md

@@ -144,7 +144,7 @@ Examples of relevant files:
 - core implementation files
 - architecture docs
 - plans
-- tracker files
+- active plan or workspace files
 - config files
 - failing or partial implementations
 - screenshots or exported artifacts when available through the current tool surface

package/templates/.agents/skills/code-guide-audit/SKILL.md

@@ -11,7 +11,7 @@ This skill owns one job: inspect the specific code the user points at, map it ag
 
 ## When Not To Use This Skill
 
-- Skip it for broad ship-readiness review; use `pre-pr-hygiene` or a ship-audit workflow for that.
+- Skip it for broad ship-readiness review; use a ship-audit workflow for that.
 - Skip it for generic bug finding or regression review that is not specifically about the coding guide.
 - Skip it for active PR comment triage; use `pr-review` for that loop.
 - Skip it for repo-wide cleanup unless the user explicitly asked for a repo-wide coding-guide audit.
@@ -52,10 +52,6 @@ Skip rules that genuinely do not apply, but say that you skipped them.
 - Do not drift into generic architecture advice, repo-wide cleanup, docs sync, or PR readiness unless the finding is directly required by the guide.
 - If you notice issues outside scope, mention them only if they are severe enough that ignoring them would mislead the user about this audit.
 
-This skill is narrower than `pre-pr-hygiene`. Use that other skill for broader ship-readiness.
-
-If this audit produces a large remediation campaign, create or update a tracker under `.waypoint/track/` before switching into implementation so the fix list does not live only in chat.
-
 ## Step 4: Verify Evidence
 
 Ground each finding in the actual code.

package/templates/.agents/skills/planning/SKILL.md

@@ -25,13 +25,12 @@ Good plans prove you understand the problem. Size matches complexity — a renam
 
 Before planning:
 
-1. Read `.waypoint/SOUL.md`
-2. Read `.waypoint/agent-operating-manual.md`
-3. Read `.waypoint/WORKSPACE.md`
-4. Read `.waypoint/ACTIVE_PLANS.md`
-5. Read `.waypoint/context/MANIFEST.md`
-6. Read every file listed in the manifest
-7. Read the routed docs relevant to the task
+1. Read `AGENTS.md`
+2. Read `.waypoint/WORKSPACE.md`
+3. Read `.waypoint/ACTIVE_PLANS.md`
+4. Read `.waypoint/DOCS_INDEX.md`
+5. Read `.waypoint/context/SNAPSHOT.md`
+6. Read the routed docs relevant to the task
 
 ## Output Location
 
@@ -40,12 +39,9 @@ The plan belongs in the repo, not only in chat.
 - Write or update a durable plan doc under `.waypoint/plans/`.
 - Choose the smallest routed location that matches the work, such as a project plan, implementation plan, or focused design note.
 - If a relevant plan doc already exists, update it instead of creating a competing one.
-- Make sure the doc remains discoverable through the routed docs layer.
 - Update `.waypoint/ACTIVE_PLANS.md` when this plan becomes the approved active plan or when its current phase changes.
 - In chat, return only a concise summary plus the path to the plan doc.
 
-If the planned implementation will be large, multi-step, or likely to span multiple sessions, also create or update a tracker under `.waypoint/track/` and link it from `WORKSPACE.md` before implementation begins.
-
 ## The Core Loop
 
 ```

package/templates/.agents/skills/pr-review/SKILL.md

@@ -10,7 +10,6 @@ Use this skill to drive the PR through review instead of treating review as a on
 ## When Not To Use This Skill
 
 - Skip it before a PR has active review or automated review in flight.
-- Skip it for local pre-push hygiene; use `pre-pr-hygiene` for that workflow.
 - Skip it for the repo-internal closeout loop on an unpushed slice; use the normal review workflows instead.
 
 ## Step 1: Wait For Review To Settle

package/templates/.codex/agents/code-health-reviewer.toml

@@ -3,11 +3,13 @@ model_reasoning_effort = "high"
 sandbox_mode = "read-only"
 developer_instructions = """
 Read these files in order before doing anything else:
-1. .waypoint/SOUL.md
-2. .waypoint/agent-operating-manual.md
-3. .waypoint/WORKSPACE.md
-4. .waypoint/context/MANIFEST.md
-5. every file listed in that manifest
+1. AGENTS.md
+2. .waypoint/WORKSPACE.md
+3. .waypoint/ACTIVE_PLANS.md
+4. .waypoint/docs/code-guide.md
+5. .waypoint/DOCS_INDEX.md
+6. .waypoint/context/SNAPSHOT.md
+7. .waypoint/context/RECENT_THREAD.md
 
 After reading them, follow these operating instructions:
 

package/templates/.codex/agents/code-reviewer.toml

@@ -3,11 +3,13 @@ model_reasoning_effort = "high"
 sandbox_mode = "read-only"
 developer_instructions = """
 Read these files in order before doing anything else:
-1. .waypoint/SOUL.md
-2. .waypoint/agent-operating-manual.md
-3. .waypoint/WORKSPACE.md
-4. .waypoint/context/MANIFEST.md
-5. every file listed in that manifest
+1. AGENTS.md
+2. .waypoint/WORKSPACE.md
+3. .waypoint/ACTIVE_PLANS.md
+4. .waypoint/docs/code-guide.md
+5. .waypoint/DOCS_INDEX.md
+6. .waypoint/context/SNAPSHOT.md
+7. .waypoint/context/RECENT_THREAD.md
 
 After reading them, follow these operating instructions:
 

package/templates/.codex/agents/plan-reviewer.toml

@@ -3,11 +3,13 @@ model_reasoning_effort = "high"
 sandbox_mode = "read-only"
 developer_instructions = """
 Read these files in order before doing anything else:
-1. .waypoint/SOUL.md
-2. .waypoint/agent-operating-manual.md
-3. .waypoint/WORKSPACE.md
-4. .waypoint/context/MANIFEST.md
-5. every file listed in that manifest
+1. AGENTS.md
+2. .waypoint/WORKSPACE.md
+3. .waypoint/ACTIVE_PLANS.md
+4. .waypoint/docs/code-guide.md
+5. .waypoint/DOCS_INDEX.md
+6. .waypoint/context/SNAPSHOT.md
+7. .waypoint/context/RECENT_THREAD.md
 
 After reading them, follow these operating instructions: