@aacombarro89/praxis 0.1.8 → 0.1.10

package/dist/shared-instructions.d.ts

@@ -0,0 +1,21 @@
+import type { Manifest } from "./manifest.js";
+/**
+ * Project-owned instructions shared by Claude Code and Codex. Unlike managed
+ * methodology blocks, these blocks carry no hash and have no generated source:
+ * both native files remain complete and editable if Praxis is removed.
+ */
+export declare const SHARED_PROJECT_BEGIN = "<!-- praxis:shared-project begin -->";
+export declare const SHARED_PROJECT_END = "<!-- praxis:shared-project end -->";
+export type SharedInstructionStatus = "not-required" | "pending-onboarding" | "missing" | "mismatch" | "synchronized";
+export interface SharedInstructionReport {
+    status: SharedInstructionStatus;
+    ok: boolean;
+    diagnostics: string[];
+}
+export declare function hasSharedProjectBlock(text: string): boolean;
+/**
+ * Check the peer-native project instruction contract. Only a dual first-class
+ * Claude+Codex install requires parity. The onboarding sentinel temporarily
+ * suspends the requirement while the agent is authoring both native surfaces.
+ */
+export declare function checkSharedInstructions(cwd: string, manifest: Manifest): SharedInstructionReport;

package/dist/shared-instructions.js

@@ -0,0 +1,63 @@
+import { existsSync, readFileSync } from "node:fs";
+import { join } from "node:path";
+/**
+ * Project-owned instructions shared by Claude Code and Codex. Unlike managed
+ * methodology blocks, these blocks carry no hash and have no generated source:
+ * both native files remain complete and editable if Praxis is removed.
+ */
+export const SHARED_PROJECT_BEGIN = "<!-- praxis:shared-project begin -->";
+export const SHARED_PROJECT_END = "<!-- praxis:shared-project end -->";
+const SHARED_PROJECT_RE = /<!--\s*praxis:shared-project\s+begin\s*-->[^\n]*\r?\n([\s\S]*?)\r?\n?<!--\s*praxis:shared-project\s+end\s*-->/g;
+function blockContents(text) {
+    const contents = [];
+    SHARED_PROJECT_RE.lastIndex = 0;
+    let match;
+    while ((match = SHARED_PROJECT_RE.exec(text)) !== null) {
+        contents.push((match[1] ?? "").replaceAll("\r\n", "\n"));
+    }
+    return contents;
+}
+export function hasSharedProjectBlock(text) {
+    return blockContents(text).length === 1;
+}
+function readIfExists(path) {
+    return existsSync(path) ? readFileSync(path, "utf8") : "";
+}
+/**
+ * Check the peer-native project instruction contract. Only a dual first-class
+ * Claude+Codex install requires parity. The onboarding sentinel temporarily
+ * suspends the requirement while the agent is authoring both native surfaces.
+ */
+export function checkSharedInstructions(cwd, manifest) {
+    if (!(manifest.targets.includes("claude-code") && manifest.targets.includes("codex"))) {
+        return { status: "not-required", ok: true, diagnostics: [] };
+    }
+    if (existsSync(join(cwd, ".praxis-setup-pending"))) {
+        return { status: "pending-onboarding", ok: true, diagnostics: [] };
+    }
+    const files = ["CLAUDE.md", "AGENTS.md"];
+    const blocks = new Map(files.map((file) => [file, blockContents(readIfExists(join(cwd, file)))]));
+    const diagnostics = [];
+    for (const file of files) {
+        const count = blocks.get(file)?.length ?? 0;
+        if (count === 0)
+            diagnostics.push(`${file}: missing project-owned praxis:shared-project block`);
+        if (count > 1)
+            diagnostics.push(`${file}: expected one praxis:shared-project block, found ${count}`);
+    }
+    if (diagnostics.length > 0)
+        return { status: "missing", ok: false, diagnostics };
+    const claude = blocks.get("CLAUDE.md")?.[0] ?? "";
+    const agents = blocks.get("AGENTS.md")?.[0] ?? "";
+    if (claude !== agents) {
+        return {
+            status: "mismatch",
+            ok: false,
+            diagnostics: [
+                "CLAUDE.md and AGENTS.md shared project blocks differ; run the Praxis upkeep workflow to reconcile project-owned facts",
+            ],
+        };
+    }
+    return { status: "synchronized", ok: true, diagnostics: [] };
+}
+//# sourceMappingURL=shared-instructions.js.map

package/dist/shared-instructions.js.map

@@ -0,0 +1 @@
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package/dist/sync.js

@@ -1,8 +1,10 @@
-import { existsSync, mkdirSync, readdirSync, readFileSync, unlinkSync, writeFileSync } from "node:fs";
+import { existsSync, mkdirSync, readdirSync, readFileSync, rmdirSync, unlinkSync, writeFileSync } from "node:fs";
 import { dirname, join } from "node:path";
 import { applyOp, BLOCK_FILE, planEmit } from "./emit.js";
 import { loadManifest } from "./manifest.js";
 import { blockStatus, findBlocks } from "./merge.js";
+import { reconcileCodexConfig } from "./codex-security.js";
+import { CODEX_MARKETPLACE_PATH, CODEX_MARKETPLACE_STATE_PATH, reconcileCodexMarketplace, } from "./codex-marketplace.js";
 export function runSync(opts) {
     const manifestPath = opts.manifestPath ?? join(opts.cwd, "praxis.yaml");
     return applyManifest(loadManifest(manifestPath), opts.cwd, opts.write);
@@ -13,11 +15,33 @@ export function runSync(opts) {
  * the emit before `praxis.yaml` exists.
  */
 export function applyManifest(manifest, cwd, write) {
-    const ops = planEmit(manifest);
+    const ops = planEmit(manifest, cwd);
     const files = [];
     const handledPaths = new Set();
     for (const op of ops) {
         handledPaths.add(op.path);
+        if (op.kind === "codex-marketplace") {
+            handledPaths.add(op.statePath);
+            const marketplaceAbs = join(cwd, op.path);
+            const stateAbs = join(cwd, op.statePath);
+            const marketplaceExisting = readFileIfExists(marketplaceAbs) ?? "";
+            const stateExisting = readFileIfExists(stateAbs) ?? "";
+            const result = reconcileCodexMarketplace(marketplaceExisting, stateExisting, op.plugins);
+            for (const output of [
+                { path: op.path, abs: marketplaceAbs, existing: marketplaceExisting, text: result.marketplaceText, changed: result.marketplaceChanged, conflicts: result.conflicts },
+                { path: op.statePath, abs: stateAbs, existing: stateExisting, text: result.stateText, changed: result.stateChanged, conflicts: [] },
+            ]) {
+                const existed = existsSync(output.abs);
+                const status = !existed ? "created" : output.changed ? "updated" : "unchanged";
+                const written = write && output.changed;
+                if (written) {
+                    mkdirSync(dirname(output.abs), { recursive: true });
+                    writeFileSync(output.abs, output.text, "utf8");
+                }
+                files.push({ path: output.path, status, conflicts: output.conflicts, written });
+            }
+            continue;
+        }
         const abs = join(cwd, op.path);
         const existing = readFileIfExists(abs);
         const result = applyOp(op, existing ?? "");
@@ -67,6 +91,62 @@ export function applyManifest(manifest, cwd, write) {
             written,
         });
     }
+    // A removed Codex permissions package/target removes only Praxis's protected
+    // TOML block; unrelated project configuration remains byte-for-byte intact.
+    const codexConfigPath = ".codex/config.toml";
+    if (!handledPaths.has(codexConfigPath)) {
+        const abs = join(cwd, codexConfigPath);
+        const existing = readFileIfExists(abs);
+        if (existing !== undefined) {
+            const result = reconcileCodexConfig(existing, false);
+            if (result.changed || result.conflicts.length > 0) {
+                const written = write && result.changed;
+                if (written)
+                    writeFileSync(abs, result.text, "utf8");
+                files.push({
+                    path: codexConfigPath,
+                    status: result.changed ? "updated" : "unchanged",
+                    conflicts: result.conflicts,
+                    written,
+                });
+            }
+        }
+    }
+    // Marketplace ownership lives in a committed sidecar. Without that state,
+    // removal is deliberately conservative: Praxis cannot prove an entry is its own.
+    if (!handledPaths.has(CODEX_MARKETPLACE_PATH)) {
+        const marketplaceAbs = join(cwd, CODEX_MARKETPLACE_PATH);
+        const stateAbs = join(cwd, CODEX_MARKETPLACE_STATE_PATH);
+        const marketplaceExisting = readFileIfExists(marketplaceAbs);
+        const stateExisting = readFileIfExists(stateAbs);
+        if (marketplaceExisting !== undefined && stateExisting !== undefined) {
+            const result = reconcileCodexMarketplace(marketplaceExisting, stateExisting, []);
+            for (const output of [
+                { path: CODEX_MARKETPLACE_PATH, abs: marketplaceAbs, text: result.marketplaceText, changed: result.marketplaceChanged, conflicts: result.conflicts },
+                { path: CODEX_MARKETPLACE_STATE_PATH, abs: stateAbs, text: result.stateText, changed: result.stateChanged, conflicts: [] },
+            ]) {
+                if (!output.changed && output.conflicts.length === 0)
+                    continue;
+                const written = write && output.changed;
+                if (written)
+                    writeFileSync(output.abs, output.text, "utf8");
+                files.push({
+                    path: output.path,
+                    status: output.changed ? "updated" : "unchanged",
+                    conflicts: output.conflicts,
+                    written,
+                });
+            }
+        }
+        else if (stateExisting !== undefined) {
+            // marketplace.json is gone (hand-deleted or never re-created) but the
+            // Praxis-owned sidecar remains — it now describes nothing and would
+            // otherwise orphan forever. Prune it (D46: manifest expresses absence).
+            if (write)
+                unlinkSync(stateAbs);
+            files.push({ path: CODEX_MARKETPLACE_STATE_PATH, status: "deleted", conflicts: [], written: write });
+        }
+    }
     // Owned-file orphans: `.claude/rules/praxis-*.md` / `.claude/commands/praxis-*.md`
     // on disk that the current manifest no longer implies (the package that used to
     // own them was removed, or its target was). The `praxis-` prefix is the
@@ -74,8 +154,13 @@ export function applyManifest(manifest, cwd, write) {
     // — acceptable because deletion is always previewed here, never silent.
     const impliedOwnedPaths = new Set(ops.filter((op) => op.kind === "owned").map((op) => op.path));
     for (const path of findOwnedOrphans(cwd, impliedOwnedPaths)) {
-        if (write)
-            unlinkSync(join(cwd, path));
+        if (write) {
+            const abs = join(cwd, path);
+            unlinkSync(abs);
+            const parent = dirname(abs);
+            if (path.startsWith(".agents/skills/") && readdirSync(parent).length === 0)
+                rmdirSync(parent);
+        }
         files.push({ path, status: "deleted", conflicts: [], written: write });
     }
     return {
@@ -93,8 +178,8 @@ function readFileIfExists(path) {
     }
 }
 // Directories whose contents are Praxis-owned by naming convention alone — see
-// `planEmit` in src/emit.ts, which only ever writes `praxis-*.md` under these two.
-const OWNED_ORPHAN_DIRS = [".claude/rules", ".claude/commands"];
+// `planEmit` in src/emit.ts; files in these directories are owned by prefix.
+const OWNED_ORPHAN_DIRS = [".claude/rules", ".claude/commands", ".codex/rules"];
 /** Praxis-owned files on disk (by the `praxis-` prefix convention) whose path is
  *  not in `impliedPaths` — the current manifest no longer emits them. */
 function findOwnedOrphans(cwd, impliedPaths) {
@@ -104,13 +189,24 @@ function findOwnedOrphans(cwd, impliedPaths) {
         if (!existsSync(abs))
             continue;
         for (const entry of readdirSync(abs, { withFileTypes: true })) {
-            if (!entry.isFile() || !entry.name.startsWith("praxis-") || !entry.name.endsWith(".md"))
+            const suffix = dir === ".codex/rules" ? ".rules" : ".md";
+            if (!entry.isFile() || !entry.name.startsWith("praxis-") || !entry.name.endsWith(suffix))
                 continue;
             const path = `${dir}/${entry.name}`;
             if (!impliedPaths.has(path))
                 orphans.push(path);
         }
     }
+    const skillsDir = join(cwd, ".agents/skills");
+    if (existsSync(skillsDir)) {
+        for (const entry of readdirSync(skillsDir, { withFileTypes: true })) {
+            if (!entry.isDirectory() || !entry.name.startsWith("praxis-"))
+                continue;
+            const path = `.agents/skills/${entry.name}/SKILL.md`;
+            if (existsSync(join(cwd, path)) && !impliedPaths.has(path))
+                orphans.push(path);
+        }
+    }
     return orphans;
 }
 /** Remove one managed block (both markers + content) from `text`, absorbing the

package/dist/sync.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aacombarro89/praxis",
-  "version": "0.1.8",
+  "version": "0.1.10",
   "description": "A CLI that installs an AI methodology layer into a codebase.",
   "type": "module",
   "bin": {

package/packages/external/ponytail/plugins.yaml

@@ -2,7 +2,7 @@
 # Praxis never executes anything here — this is committable config that Claude
 # Code itself reads on folder-trust to offer installing/enabling the plugin.
 # Verified against github.com/DietrichGebert/ponytail (tag v4.7.0 exists).
-targets: [claude-code]
+targets: [claude-code, codex]
 marketplace:
   name: ponytail
   source:
@@ -11,3 +11,6 @@ marketplace:
     ref: v4.7.0
 enable:
   - ponytail@ponytail
+codex:
+  name: ponytail
+  category: Developer Tools

package/packages/layer1/capture-codebase-patterns/commands/capture-codebase-patterns.md

@@ -0,0 +1,68 @@
+---
+description: Capture this team's own coding patterns from an exemplar module into a project-local Praxis package that rides praxis sync.
+argument-hint: [optional-exemplar-path]
+allowed-tools: Read, Glob, Grep, Bash(git log:*), Bash(git diff:*), Bash(ls:*), Bash(mkdir:*), Write, Edit, Bash(npx @aacombarro89/praxis@latest sync:*), Bash(npx @aacombarro89/praxis@latest check:*), Bash(npx @aacombarro89/praxis sync:*), Bash(npx @aacombarro89/praxis check:*), Bash(praxis sync:*), Bash(praxis check:*)
+---
+
+Exemplar: {{arguments}} — if empty, propose candidates in step 2 rather than
+picking silently.
+
+Praxis never calls an LLM (D12) or authors project facts directly (D13). The
+**agent** — you — extracts and authors every pattern below *with the user*;
+Praxis's own CLI only resolves, emits, and syncs the package once it exists.
+
+1. **Preflight.** Read `praxis.yaml` (`targets`, `stacks`, `packages`). If a
+   `./`-prefixed entry already resolves to a local patterns package (its
+   `package.yaml` under `praxis/packages/<name>/`), this is a refinement run:
+   read its `rules.md` and offer to update or extend it rather than create a
+   new one. State the framing above up front so the user knows what's about to
+   happen.
+
+2. **Exemplar interview.** Ask the user to point at one to three modules or
+   directories that best show how code in this repo *should* look. If they
+   can't choose, propose candidates — central, recently and frequently touched
+   directories — and confirm before proceeding, never pick silently:
+
+   - Recently touched: {{shell:git log --oneline -20 2>/dev/null}}
+   - Frequently touched: {{shell:git log --pretty=format: --name-only -50 2>/dev/null | sort | uniq -c | sort -rn | head -20}}
+
+3. **Extract candidates.** Read the exemplar(s), their immediate neighbors,
+   and their tests. Derive candidate patterns across this checklist: module
+   structure & naming, import/dependency habits, error handling,
+   typing/validation, IO-vs-logic separation, test shape & location,
+   comment/doc style. Every candidate cites concrete evidence — the file and
+   the shape in it that shows the pattern. Never propose a pattern the code
+   does not actually exhibit.
+
+4. **Iterate.** Present candidates in small groups; the user accepts, rejects,
+   or refines each. When a candidate is a recognized anti-pattern, push back
+   once with rationale — what breaks, and when — then let the user decide; if
+   they keep it, record it plainly rather than silently dropping the pushback.
+   A convention enters the package only if it's verifiable in the exemplar or
+   explicitly confirmed by the user.
+
+5. **Scaffold the local package.** Default to
+   `praxis/packages/codebase-patterns/`; confirm the name with the user
+   (kebab-case — the declared `name` must equal the directory basename, same
+   rule as a shipped package). Write:
+
+   - `package.yaml` — `name`, `layer: local`, `provides: [rules]`.
+   - `rules.md` — compact imperative bullets, each with a one-line why and an
+     exemplar pointer (`path` — what it shows). Aim under ~60 lines; this file
+     is always-loaded once installed, so keep it to what earns that cost. Use
+     `paths:` frontmatter only if the conventions are scoped to a subtree.
+
+6. **Register.** Add `./praxis/packages/codebase-patterns` (or the confirmed
+   path) to the `packages:` list in `praxis.yaml`. Editing the manifest and
+   syncing is the only customization path — never write emitted files by hand.
+
+7. **Sync + verify.** Run `praxis sync` if the CLI is on PATH, otherwise fall
+   back to `npx @aacombarro89/praxis@latest sync` (pin `@latest` — a bare
+   `npx @aacombarro89/praxis` can silently reuse a stale cached build). Then
+   run `praxis check` (or the `npx` equivalent) and fix anything it reports
+   before finishing.
+
+8. **Report.** Summarize the conventions captured (with their exemplar
+   pointers), any candidates the user rejected and why, and note that this
+   command is re-runnable anytime to refine or extend the package as the
+   codebase evolves.

package/packages/layer1/capture-codebase-patterns/package.yaml

@@ -0,0 +1,14 @@
+# Package manifest (docs/wiki/packages-and-emit.md, D49). Commands-only: no rules.md,
+# so this package is zero-cost between runs (nothing always-loaded). Ships the
+# /praxis-capture-codebase-patterns command (commands/capture-codebase-patterns.md):
+# the agent interviews the developer, extracts this team's OWN coding patterns from an
+# exemplar module with cited evidence, iterates on candidates, and generates a
+# project-local `codebase-patterns` package (layer: local, D49) that then rides normal
+# `praxis sync`. Praxis never calls an LLM or authors project facts directly (D12/D13) —
+# the agent authors the generated package's content, guided by this command.
+name: capture-codebase-patterns
+layer: layer1
+provides: [commands]
+onboarding:
+  command: praxis-capture-codebase-patterns
+  summary: "Capture this team's own coding patterns from an exemplar module into a project-local Praxis package that rides praxis sync."

package/packages/layer1/instruction-upkeep/commands/instructions.md

@@ -1,14 +1,16 @@
 ---
-description: Keep the authored instruction files (CLAUDE.md, .claude/rules) current with the project's state and complete against the standard rubric.
+description: Keep the project's authored agent instruction files current with its state and complete against the standard rubric.
 ---
 
-Scope: $ARGUMENTS
+Scope: {{arguments}}
 
-This updates the **authored instruction layer** — `CLAUDE.md` and
-`.claude/rules` — not the tool's native auto-memory and not any 3rd-party
+This updates the **authored agent instruction layer** — project-owned prose in
+the selected tool's instruction surfaces — not native auto-memory and not any 3rd-party
 agent-memory system. Those are out of scope.
 
-1. Read `CLAUDE.md` and every file under `.claude/rules`. Identify any
+1. Read `praxis.yaml`, then read every project instruction surface selected by
+   its first-class targets (`CLAUDE.md` for Claude Code, `AGENTS.md` for Codex).
+   Identify any
    canonical doc they point to (architecture doc, decision log, design doc).
 2. Compare what the instruction files claim against that canonical doc and
    against recent git history (`git log`, changed files) and the current
@@ -21,6 +23,11 @@ agent-memory system. Those are out of scope.
    - always-do rules (the few non-negotiable habits)
 
    Flag any rubric section that's entirely absent, citing where it should go.
+   When Claude Code and Codex are both selected, inspect the project-owned
+   `praxis:shared-project` block in both native files. Their contents must match
+   exactly (apart from line endings), while prose outside the blocks may differ.
+   Treat a missing, duplicate, or mismatched block reported by `praxis check` as
+   authored instruction drift — never choose one file as the automatic winner.
 3. **Ask the user before editing anything.** Present the list from step 2 and
    confirm which items to fix.
 4. For approved items, update only project-owned sections of the instruction
@@ -28,6 +35,8 @@ agent-memory system. Those are out of scope.
    code, or the user's answer. Where an instruction file currently restates a
    fact that lives in a canonical doc, prefer replacing the restatement with a
    link to that doc (reference, don't duplicate) so it can't drift again.
+   In a dual-target repo, apply approved shared-fact changes to both shared blocks
+   together and preserve all target-specific content outside them.
 5. If an instruction file carries `praxisAnchors` frontmatter, revalidate and
    update the anchors for any changed source reference. Phase-2 anchors are
    deterministic only:

package/packages/layer1/instruction-upkeep/rules.md

@@ -1,10 +1,14 @@
 ## Instruction upkeep
 
-The authored instruction layer (`CLAUDE.md`, `.claude/rules`) drifts as a
+The authored agent instruction layer drifts as a
 project changes. When it goes stale, incomplete, or a misunderstanding
 surfaces, fix it — checking coverage against: build/test/run commands ·
 layout · conventions · always-do rules.
 
-Make changes through `/praxis-instructions`, not ad-hoc edits. When
+When multiple first-class targets are selected, audit every native project
+instruction surface. Shared project sections must remain consistent; native
+target-specific sections may differ.
+
+Make changes through `{{workflow:praxis-instructions}}`, not ad-hoc edits. When
 reconciling the methodology layer after a change, enter through
-`/praxis-upkeep` (which delegates here) instead of running this pass alone.
+`{{workflow:praxis-upkeep}}` (which delegates here) instead of running this pass alone.

package/packages/layer1/onboarding/commands/onboard.md

@@ -1,24 +1,37 @@
 ---
-description: Author the project-owned sections of CLAUDE.md for a fresh Praxis install — build/run/test commands, layout, conventions, and always-do rules. One-shot: deletes .praxis-setup-pending when done.
+description: Author project-owned agent instructions for a fresh Praxis install—build/run/test commands, layout, conventions, and always-do rules. One-shot: deletes .praxis-setup-pending when done.
 ---
 
-Scope: $ARGUMENTS
+Scope: {{arguments}}
 
 This is the **first-run front gate** — the single entry point for a fresh Praxis
-install, symmetric to `/praxis-upkeep` (the ongoing front gate). It authors the
-**project-owned** sections of `CLAUDE.md`, then seeds the installed methodology
-packages, then hands off to `/praxis-upkeep` so the full baseline is established
+install, symmetric to `{{workflow:praxis-upkeep}}` (the ongoing front gate). It authors
+the **project-owned** agent instructions, then seeds the installed methodology
+packages, then hands off to `{{workflow:praxis-upkeep}}` so the full baseline is established
 in one pass.
 
-Praxis never calls an LLM (D12); never edits `CLAUDE.md` directly (D13). The
+Praxis never calls an LLM (D12) or authors project facts directly (D13). The
 **agent** writes the facts, guided by the steps below, asking the user for
 anything it cannot infer.
 
-1. **Bulk discovery — lean on the tool's native `/init` first.** If `CLAUDE.md`
-   does not yet exist (or is empty), suggest running the tool's built-in `/init`
-   command so the model can auto-discover repository facts (files, build config,
-   README). Incorporate any useful output into the project-owned sections below,
-   rather than restating it from scratch.
+1. **Choose the project instruction surfaces from `praxis.yaml`.** For a Codex-only
+   install, author project facts as free prose outside managed blocks in `AGENTS.md`.
+   For Claude-only, retain the existing `CLAUDE.md` flow. When both are selected,
+   maintain both native files as peers — never make either import or replace the
+   other. Put facts shared by both tools inside exactly one project-owned block in
+   each file, with identical content and these marker lines:
+
+   ```markdown
+   <!-- praxis:shared-project begin -->
+   ...shared project facts...
+   <!-- praxis:shared-project end -->
+   ```
+
+   The markers declare a parity contract, not Praxis ownership: the project owns
+   the prose and both native files remain complete if Praxis is removed. Guidance
+   outside this block may differ by target. If the active tool offers a native
+   repository initialization workflow, suggest it for bulk discovery and
+   incorporate useful output rather than re-deriving it.
 
 2. **Check detected stacks (if known).** Read `praxis.yaml` for the `stacks:`
    field. If stacks are declared, tailor the sections below to those stacks (e.g.
@@ -44,30 +57,35 @@ anything it cannot infer.
      short; a long always-do list is never read.
 
 4. **Ask the user for anything not inferable.** If a section can't be filled from
-   config files, git history, or the `/init` output, ask a targeted question
-   rather than inventing a plausible answer. Content inclusion bar: a fact only
-   enters if it's backed by the code, config, a canonical doc, or the user.
+   config files, git history, or the native initialization workflow's output, ask
+   a targeted question rather than inventing a plausible answer. Content
+   inclusion bar: a fact only enters if it's backed by the code, config, a
+   canonical doc, or the user.
 
 5. **Write only project-owned content.** Never put content inside a Praxis
-   managed block (a `<!-- praxis-start … -->` / `<!-- praxis-end … -->` region).
-   Project facts belong in the free-prose sections the author controls; Praxis
-   owns only its own managed blocks.
+   managed block (a `<!-- praxis:begin … -->` / `<!-- praxis:end … -->` region).
+   Project facts belong in the free-prose sections the author controls; the
+   unhashed `praxis:shared-project` block is also project-owned. Praxis owns only
+   its hashed managed blocks. When both native files are selected, write the four
+   rubric sections to both shared blocks in one edit and keep their content exact.
 
 6. **Run each installed companion bootstrap action** (each seeds part of the
-   methodology), then hand off to `/praxis-upkeep`:
+   methodology), then hand off to `{{workflow:praxis-upkeep}}`:
 
 <!-- praxis:bootstrap-delegations -->
 
-   After the bootstrap actions above complete, run `/praxis-upkeep` to confirm
-   the full methodology baseline is in sync. If `/praxis-upkeep` is not
+   After the bootstrap actions above complete, run `{{workflow:praxis-upkeep}}` to confirm
+   the full methodology baseline is in sync. If `{{workflow:praxis-upkeep}}` is not
    installed, skip this step.
 
 7. **Delete `.praxis-setup-pending`** to make this one-shot. Once the rubric
-   sections are authored and the user is satisfied, remove the sentinel file
-   from the repo root. This prevents the bootstrap rule (`.claude/rules/
-   praxis-onboarding.md`) from re-offering onboarding on the next session.
+   sections are authored, the bootstrap actions and upkeep pass above have run,
+   and the user is satisfied, remove the sentinel file from the repo root. This
+   prevents the bootstrap rule from re-offering onboarding on the next session —
+   deleting it any earlier would leave an interrupted session with no re-offer
+   and an unseeded baseline.
 
 8. **Report what was written / left.** Summarise which rubric sections were
    filled, which were left empty (and why — e.g. "no build step detected"), and
    any follow-up items for the user. The baseline is now established; from here
-   `/praxis-upkeep` keeps the methodology layer current.
+   `{{workflow:praxis-upkeep}}` keeps the methodology layer current.

package/packages/layer1/onboarding/rules.md

@@ -1,10 +1,10 @@
 ## First-run onboarding
 
 At the start of work, check for the `.praxis-setup-pending` sentinel file in
-the repo root: present means a fresh Praxis install whose project-owned
-`CLAUDE.md` sections aren't authored yet.
+the repo root: present means a fresh Praxis install whose project-owned agent
+instruction sections aren't authored yet.
 
-- **Present:** offer to run `/praxis-onboard`; it deletes the sentinel on
+- **Present:** offer to run `{{workflow:praxis-onboard}}`; it deletes the sentinel on
   completion, making this check one-shot. Never nag when absent.
-- **Absent:** do nothing here — `/praxis-upkeep` (ongoing front gate, D29/D31)
+- **Absent:** do nothing here — `{{workflow:praxis-upkeep}}` (ongoing front gate, D29/D31)
   handles currency after initial setup.

package/packages/layer1/safe-permissions/permissions.yaml

@@ -1,7 +1,7 @@
 # Neutral permission policy — the enforcement side of the rails
 # (docs/wiki/emitters.md, D18/D19). Tool-agnostic INTENT expressed as capabilities; per-tool emitters
-# translate to concrete rule strings (Claude Code today; tools without a
-# permission model emit nothing). Edit your own settings to tune — Praxis owns
+# translate to target-native Claude Code and Codex controls; tools without a
+# permission model emit nothing. Edit your own settings to tune — Praxis owns
 # only the rules it emits and never clobbers rules you add.
 #
 # Posture: allow common local dev (smooth); prompt before anything that leaves the

package/packages/layer1/session-handoff/commands/handoff.md

@@ -46,10 +46,10 @@ single-doc flow below.
 
 Read the clock so the name sorts chronologically (do not guess the time):
 
-- Timestamp: !`date +%Y-%m-%d_%H%M`
+- Timestamp: {{shell:date +%Y-%m-%d_%H%M}}
 
 Build the filename `YYYY-MM-DD_HHMM_HANDOFF_<topic>.md`:
-- `<topic>` is a short kebab-case slug for the work. Use `$ARGUMENTS` if
+- `<topic>` is a short kebab-case slug for the work. Use {{arguments}} if
   provided; otherwise derive it from the task.
 - Date-and-time first means a plain alphabetical listing is chronological.
 
@@ -73,9 +73,9 @@ references* section below. Don't re-derive them; you already paid for them.
 If in a git repo, capture current branch, staged/unstaged changes, and recent
 commits from this session:
 
-- Branch: !`git branch --show-current 2>/dev/null`
-- Status: !`git status --short 2>/dev/null`
-- Recent commits: !`git log --oneline -10 2>/dev/null`
+- Branch: {{shell:git branch --show-current 2>/dev/null}}
+- Status: {{shell:git status --short 2>/dev/null}}
+- Recent commits: {{shell:git log --oneline -10 2>/dev/null}}
 
 Capture verification state too: identify the project's own build/test/lint
 commands (from its config / docs / CI) and record their current result — what