feat(system): bind cubefs+cubecode+cubecrypt into one running system (cubesys)

Integrates Packages 3-5 over a single shared CubeStore, the literal
CUBELinux premise (data addressed by coordinate, not path). Adds the
cubesys crate (lib + cube CLI + cube-demo) proving two end-to-end
properties: a cubefs path IS a runnable code cell at the same coordinate,
and a sealed record reopens and runs on the same store.

Two latent cross-crate bugs surfaced and fixed while integrating:
- cubecoords: refresh_flags() now preserves out-of-band flag bits
  (8..=15), so cubecrypt's HEADER_FLAG_ENCRYPTED survives refresh.
- cubestore: record codec now serializes raw flag bits (TLV tag 12) so
  the encrypted bit survives the store round-trip.

All gates green (./check, incl. cubefs --features mount).

Cargo.toml

@@ -6,6 +6,7 @@ members = [
     "cubefs",
     "cubecode",
     "cubecrypt",
+    "cubesys",
 ]
 
 [workspace.package]

cubecoords/src/lib.rs

@@ -194,6 +194,13 @@ impl HeaderFlags {
         HeaderFlags(bits)
     }
 
+    /// Alias for [`from_bits`] used by record decoders that reconstruct a
+    /// header's raw flag field.
+    #[inline]
+    pub const fn flags_from_bits(bits: u16) -> Self {
+        HeaderFlags(bits)
+    }
+
     /// The raw bitmask.
     #[inline]
     pub const fn bits(&self) -> u16 {
@@ -256,6 +263,12 @@ impl CubeHeader {
 
     /// Recompute the flag bits from which fields are present. Call after
     /// mutating fields so `flags` stays consistent with the structure.
+    ///
+    /// Known field flags occupy bits 0–7 (title..associations). Any
+    /// out-of-band/spare bits set directly on `flags` (e.g.
+    /// `cubecrypt::HEADER_FLAG_ENCRYPTED` at bit 12) are preserved, because
+    /// they are not derived from structured fields and would otherwise be
+    /// clobbered on every refresh.
     pub fn refresh_flags(&mut self) {
         let mut f = 0u16;
         if self.title.is_some() {
@@ -279,6 +292,10 @@ impl CubeHeader {
         if !self.linked_records.is_empty() {
             f |= HeaderFlags::HAS_ASSOCIATIONS;
         }
+        // Preserve spare/out-of-band flag bits (bits 8..=15) that are not
+        // derived from structured fields.
+        const DERIVED_BITS: u16 = 0x00FF;
+        f |= self.flags.bits() & !DERIVED_BITS;
         self.flags = HeaderFlags::from_bits(f);
     }
 }

cubecrypt/src/lib.rs

@@ -38,22 +38,22 @@ pub use env::{CubeEnv, EnvError, Selector, HEADER_FLAG_ENCRYPTED};
 pub use transform::{CryptoError, Key, KeySlot, TransformId};
 
 use cubecoords::{CubeHeader, Czyx};
-use cubestore::{CubeStore, HashBackend};
+use cubestore::{CubeBackend, CubeStore};
 
 /// An append-only access log living in a Null-cube range. Each [`AccessLog`]
 /// targets one Null-cube head coordinate and appends fixed-size entries
 /// (record coord + op byte + 8-byte timestamp). It is "tamper-evident" in the
 /// weak sense that the log itself can be stored encrypted via another
 /// [`CubeEnv`]; this type only provides the structure and append/read.
-pub struct AccessLog {
-    store: CubeStore<HashBackend>,
+pub struct AccessLog<B: CubeBackend> {
+    store: CubeStore<B>,
     head: Czyx,
     next: u8,
 }
 
-impl AccessLog {
+impl<B: CubeBackend> AccessLog<B> {
     /// Bind a log to a Null-cube head coordinate (entries append along X).
-    pub fn new(store: CubeStore<HashBackend>, head: Czyx) -> Self {
+    pub fn new(store: CubeStore<B>, head: Czyx) -> Self {
         AccessLog {
             store,
             head,

cubestore/src/lib.rs

@@ -64,6 +64,7 @@ pub trait CubeBackend {
 /// Decision: packs to `u32` (not a 4-tuple key) so the map layout matches the
 /// PDF's `HashMap<u32, Vec<u8>>` example exactly and stays cheap. A production
 /// backend would replace this with the on-disk store.
+#[derive(Clone)]
 pub struct HashBackend(pub HashMap<u32, Vec<u8>>);
 
 impl HashBackend {
@@ -106,6 +107,7 @@ impl CubeBackend for HashBackend {
 /// The header is length-prefixed so the body boundary is recoverable without
 /// a fixed schema — this is the "evolve toward explicit C/Z/Y/X-mapped flag
 /// bytes" step the PDF mentions, done inline.
+#[derive(Clone)]
 pub struct CubeStore<B: CubeBackend> {
     backend: B,
 }
@@ -180,6 +182,13 @@ mod record_codec {
         if let Some(a) = h.last_remote_access {
             put_u64(&mut out, 11, a);
         }
+        // Tag 12: raw flag bits. Serializes out-of-band/spare bits (e.g.
+        // `cubecrypt::HEADER_FLAG_ENCRYPTED`) that are not derived from
+        // structured fields, so they survive an encode/decode round-trip.
+        if h.flags.bits() != 0 {
+            out.push(12);
+            out.extend_from_slice(&h.flags.bits().to_le_bytes());
+        }
         out
     }
 
@@ -257,6 +266,14 @@ mod record_codec {
                     h.last_remote_access = Some(v);
                     b = rest;
                 }
+                12 => {
+                    if b.len() < 2 {
+                        return None;
+                    }
+                    let raw = u16::from_le_bytes([b[0], b[1]]);
+                    h.flags = cubecoords::HeaderFlags::flags_from_bits(raw);
+                    b = &b[2..];
+                }
                 _ => return None, // unknown tag -> reject (strict at Package 1)
             }
         }

cubesys/Cargo.toml

@@ -0,0 +1,21 @@
+[package]
+name = "cubesys"
+version = "0.1.0"
+edition.workspace = true
+license.workspace = true
+description = "CUBELinux-2 system integration: one CubeStore shared by cubefs, cubecode and cubecrypt (PDF Packages 3-5 bound into a single running system)."
+
+[dependencies]
+cubecoords = { path = "../cubecoords" }
+cubestore = { path = "../cubestore" }
+cubefs = { path = "../cubefs" }
+cubecode = { path = "../cubecode" }
+cubecrypt = { path = "../cubecrypt" }
+
+[[bin]]
+name = "cube"
+path = "src/bin/cube.rs"
+
+[[bin]]
+name = "cube-demo"
+path = "src/bin/cube_demo.rs"

cubesys/docs/integration.md

@@ -0,0 +1,90 @@
+# CUBELinux-2 system integration (`cubesys`)
+
+This crate is the composition layer the PDF implies but does not name as a
+"Package 6". It binds Packages 3-5 (cubefs, cubecode, cubecrypt) into one
+running system over a **single shared `CubeStore`**, which is the literal
+CUBELinux premise: *data addressed by coordinate, not path.*
+
+## The one invariant
+
+> The cube is the single source of truth. cubefs is a *view* of it, cubecode
+> is a *kind* of record in it, cubecrypt is a *transform* applied to records
+> in it. None of them own storage.
+
+That is what makes the integration real instead of three crates side by side:
+every layer operates on the same backend, so a write through one is visible to
+the others at the same coordinate.
+
+## What binds to what
+
+| Layer        | Role in the system                                   | Shares via                       |
+|--------------|------------------------------------------------------|----------------------------------|
+| `cubefs`     | POSIX namespace; a path `C/Z/Y/X` is a coordinate    | `CubeStore`, `path_to_czyx`      |
+| `cubecode`   | code cells stored *as records*; VM runs them         | `CubeStore`, `CodeCell`          |
+| `cubecrypt`  | seals records under a `CubeEnv`; key in Null cubes    | `CubeStore`, `CubeEnv`           |
+
+Two primitives in this crate do the binding:
+
+* `path_to_czyx(path)` — the single bijection (re-exported from `cubefs`) so
+  path and coordinate never disagree.
+* `load_code_cell(store, path)` — reads the record at a path's coordinate and
+  decodes it as cubevm bytecode. A cubefs file **is** a runnable VM cell.
+
+## End-to-end properties proved by the tests
+
+1. **A path is a function.** Writing bytecode at `/c012/z001/y001/x021` makes
+   cubefs list it as a file *and* the VM run it at `Czyx::new(12,1,1,21)` —
+   same coordinate, two views. (Note: an axis value of `0` is Null control
+   space and is rejected as a path component, so every user path maps to a
+   coordinate with all axes in `1..=255`; keys and metadata live in Null
+   space and are addressed directly by `C.Z.Y.X`.)
+2. **Seal then run is the same record.** `CubeEnv::put_encrypted` at a
+   coordinate leaves the cube carrying an encrypted body (encrypted flag set);
+   the raw body no longer decodes as bytecode. To *execute* a sealed record the
+   system decrypts it back into a plaintext record at the same coordinate, then
+   runs the VM (the VM runs code located by coordinate; reading the envelope
+   directly would fail decode). `open` + `CodeCell::from_record` + `Vm::run`
+   recovers and executes it on the *same* store.
+
+## Bugs found and fixed while integrating (real, cross-crate)
+
+Building the integration turned up two latent cross-crate bugs that the
+per-package test suites never exercised:
+
+* **`CubeHeader::refresh_flags()` dropped out-of-band flag bits.** It recomputed
+  `flags` only from structured fields (bits 0–7), so `cubecrypt`'s
+  `HEADER_FLAG_ENCRYPTED` (bit 12), which is set out-of-band, was wiped on every
+  refresh. `put_encrypted` calls `refresh_flags` before storing, so an encrypted
+  record lost its flag. Fixed by preserving spare bits (8..=15) in
+  `refresh_flags`. (`cubecoords`)
+* **The record codec never serialized `flags`.** `record_codec::encode_header`
+  wrote only structured fields, and `decode_header` rebuilt `flags` from them —
+  so even a correctly-set encrypted bit was lost on the store round-trip. Added
+  tag `12` (raw flag bits) to the TLV codec so out-of-band bits survive.
+  (`cubestore`)
+
+Both are now guarded by `cubesys` integration tests.
+
+## Why this, and not a "Package 6"
+
+The PDF arc ends at cubecrypt; the only named next package is `cubeai`, which
+the directive explicitly excluded (hardware cannot run it). Integration is the
+honest completion: it turns five isolated crates into the coherent
+coordinate-addressed system the design describes, without inventing a package
+the spec never defined.
+
+## Binaries
+
+* `cube-demo` — self-contained tour (write two linked cells, run; seal a
+  record, reopen + run). Prints evidence at each step.
+* `cube` — CLI: `write`, `run`, `ls`, `stat`, `seal`, `open` over one store,
+  interactively (`repl`), from a file (`script`), or as the demo (`demo`).
+
+## Building / testing
+
+```sh
+cd /home/CUBELinux/CUBELinux-2
+./check quick      # fmt + clippy -D warnings + tests (the gate)
+./check mount      # also builds cubefs --features mount (FUSE adapter)
+cargo run -p cubesys --bin cube-demo
+```

cubesys/src/bin/cube.rs

@@ -0,0 +1,311 @@
+//! `cube` — the CUBELinux-2 system CLI.
+//!
+//! One process holds ONE in-memory `CubeStore` shared by cubefs, cubecode and
+//! cubecrypt. Commands are issued as a script (file) or interactively (REPL);
+//! every command operates on that shared store, so `write` then `run` then
+//! `seal` then `open` all see the same cube.
+//!
+//! Usage:
+//!   cube                 # print this help
+//!   cube demo            # run the built-in integration demo
+//!   cube repl            # read commands from stdin, one per line
+//!   cube script <file>   # read commands from <file>, one per line
+//!
+//! Commands (operate on the shared cube):
+//!   write <path> <bytes...>        # store cubevm bytecode (hex/dec) at a path
+//!   run   <path>                  # load the code cell at <path> and run the VM
+//!   ls    <dir>                   # list a cubefs directory
+//!   stat  <path>                  # getattr via cubefs
+//!   seal  <path> <K.C.Z.Y.X> <tf> # encrypt the record at <path> (tf: none|gcm|chacha|xts)
+//!   open  <path> <K.C.Z.Y.X> <tf> # decrypt + decode + run the sealed record
+//!
+//! Coordinates are written `C.Z.Y.X` (decimal). Key cells live in Null space,
+//! so they are given directly as coordinates, not as cubefs paths.
+
+use std::io::BufRead;
+
+use cubecode::{CodeCell, Kind, Op, Vm};
+use cubecoords::CubeHeader;
+use cubecrypt::{CubeEnv, KeySlot, Selector, TransformId};
+use cubestore::{CubeStore, HashBackend};
+
+fn main() {
+    let args: Vec<String> = std::env::args().collect();
+    match args.get(1).map(|s| s.as_str()) {
+        None => print_help(),
+        Some("demo") => cubesys::demo::run(),
+        Some("repl") => {
+            let mut store = CubeStore::new(HashBackend::new());
+            let stdin = std::io::stdin();
+            let lock = stdin.lock();
+            for line in lock.lines() {
+                let line = match line {
+                    Ok(l) => l,
+                    Err(_) => break,
+                };
+                if line.trim().is_empty() || line.starts_with('#') {
+                    continue;
+                }
+                match run_line(&mut store, &line) {
+                    Ok(out) => println!("{out}"),
+                    Err(e) => eprintln!("error: {e}"),
+                }
+            }
+        }
+        Some("script") => {
+            let file = args.get(2).expect("script needs <file>");
+            let text = std::fs::read_to_string(file).expect("cannot read script file");
+            let mut store = CubeStore::new(HashBackend::new());
+            for line in text.lines() {
+                if line.trim().is_empty() || line.starts_with('#') {
+                    continue;
+                }
+                match run_line(&mut store, line) {
+                    Ok(out) => println!("{out}"),
+                    Err(e) => {
+                        eprintln!("error: {e}");
+                        std::process::exit(1);
+                    }
+                }
+            }
+        }
+        Some(other) => {
+            eprintln!("unknown subcommand: {other}\n");
+            print_help();
+            std::process::exit(2);
+        }
+    }
+}
+
+fn print_help() {
+    println!(
+        "cube - CUBELinux-2 system CLI (cubefs + cubecode + cubecrypt over one store)\n\
+         \n\
+         Usage:\n  \
+           cube                show this help\n  \
+           cube demo           run the built-in integration demo\n  \
+           cube repl           read commands from stdin (one per line)\n  \
+           cube script <file>  run commands from a file\n\
+         \nCommands:\n  \
+           prog  <path> <ops...>        write CUBEVM bytecode from op names\n  \
+           write <path> <bytes...>        store cubevm bytecode at a path\n  \
+           run   <path>                  run the code cell at <path>\n  \
+           ls    <dir>                   list a cubefs directory\n  \
+           stat  <path>                  getattr via cubefs\n  \
+           seal  <path> <K.Z.Y.X> <tf>   encrypt a record (tf: none|gcm|chacha|xts)\n  \
+           open  <path> <K.Z.Y.X> <tf>   decrypt + decode + run a sealed record\n"
+    );
+}
+
+/// Execute one command line against the shared store.
+fn run_line(store: &mut CubeStore<HashBackend>, line: &str) -> Result<String, String> {
+    let mut it = line.split_whitespace();
+    let cmd = it.next().ok_or_else(|| "empty line".to_string())?;
+    match cmd {
+        "prog" => {
+            // prog <path> <ops...>  — write CUBEVM bytecode assembled from
+            // op names (see `parse_op`). Example:
+            //   prog /c005/z001/y001/x007 const 7 halt
+            let path = it.next().ok_or_else(|| "prog needs <path>".to_string())?;
+            let mut ops: Vec<Op> = Vec::new();
+            while let Some(tok) = it.next() {
+                let arg = if takes_arg(tok) {
+                    it.next()
+                        .and_then(|a| a.parse::<u8>().ok())
+                        .ok_or_else(|| format!("prog: {tok} needs a u8 argument"))?
+                } else {
+                    0
+                };
+                ops.push(make_op(tok, arg)?);
+            }
+            if ops.is_empty() {
+                return Err("prog: no ops given".to_string());
+            }
+            let name = path.rsplit('/').next().unwrap_or(path);
+            let coord = cubesys::store_code_cell(store, path, Kind::Fn, name, &[], &ops)
+                .map_err(|e| e.to_string())?;
+            Ok(format!(
+                "wrote program {path} -> coord {} ({} ops)",
+                coord.pack_u32(),
+                ops.len()
+            ))
+        }
+        "write" => {
+            let path = it.next().ok_or_else(|| "write needs <path>".to_string())?;
+            let bytes: Vec<u8> = it
+                .map(parse_byte)
+                .collect::<Option<_>>()
+                .ok_or_else(|| "write: every byte must be hex/dec 0..255".to_string())?;
+            let code =
+                cubecode::decode(&bytes).map_err(|e| format!("bytecode decode error: {e:?}"))?;
+            let name = path.rsplit('/').next().unwrap_or(path);
+            let coord = cubesys::store_code_cell(store, path, Kind::Fn, name, &[], &code)
+                .map_err(|e| e.to_string())?;
+            Ok(format!("wrote {path} -> coord {}", coord.pack_u32()))
+        }
+        "run" => {
+            let path = it.next().ok_or_else(|| "run needs <path>".to_string())?;
+            let cell = cubesys::load_code_cell(store, path).map_err(|e| e.to_string())?;
+            let mut vm = Vm::new(store.clone());
+            let res = vm.run(cell.label);
+            let mut out = format!("run {path} => {res:?}");
+            if !vm.output().is_empty() {
+                out.push_str(&format!(
+                    "\n  trace: {}",
+                    String::from_utf8_lossy(vm.output()).trim_end()
+                ));
+            }
+            Ok(out)
+        }
+        "ls" => {
+            let dir = it.next().ok_or_else(|| "ls needs <dir>".to_string())?;
+            let fs = cubefs::CubeFs::new(store.clone());
+            let entries = fs.readdir(dir).map_err(|e| format!("ls {dir}: {e:?}"))?;
+            if entries.is_empty() {
+                Ok(format!("ls {dir} -> (empty)"))
+            } else {
+                let names: Vec<String> = entries.into_iter().map(|(n, _)| n).collect();
+                Ok(format!("ls {dir} -> {}", names.join("  ")))
+            }
+        }
+        "stat" => {
+            let path = it.next().ok_or_else(|| "stat needs <path>".to_string())?;
+            let fs = cubefs::CubeFs::new(store.clone());
+            let a = fs
+                .getattr(path)
+                .map_err(|e| format!("stat {path}: {e:?}"))?;
+            Ok(format!(
+                "stat {path} -> ino={} kind={:?} size={} mode={:o}",
+                a.ino, a.kind, a.size, a.mode
+            ))
+        }
+        "seal" | "open" => {
+            let path = it.next().ok_or_else(|| format!("{cmd} needs <path>"))?;
+            let keyc = it
+                .next()
+                .ok_or_else(|| format!("{cmd} needs <K.Z.Y.X> key cell"))?;
+            let tf = it
+                .next()
+                .ok_or_else(|| format!("{cmd} needs <transform>"))?;
+            let coord = cubesys::path_to_czyx(path).map_err(|e| e.to_string())?;
+            let kc =
+                parse_coord(keyc).ok_or_else(|| "bad key-cell coord (use C.Z.Y.X)".to_string())?;
+            let transform = parse_transform(tf)
+                .ok_or_else(|| "unknown transform (none|gcm|chacha|xts)".to_string())?;
+
+            // Ensure key material exists at the Null-cube key cell.
+            if store.get_record(&kc).is_none() {
+                store.put_record(kc, &CubeHeader::new(), b"demo-key-material-32-bytes-long!!");
+            }
+            let env = CubeEnv::new(
+                vec![KeySlot {
+                    key_cell: kc,
+                    transform,
+                    salt: vec![],
+                }],
+                vec![],
+            );
+
+            if cmd == "seal" {
+                let (h, body) = store
+                    .get_record(&coord)
+                    .ok_or_else(|| format!("seal: no record at {path}"))?;
+                env.put_encrypted(store, coord, Selector::Slot(0), &body, h)
+                    .map_err(|e| format!("seal: {e:?}"))?;
+                Ok(format!("sealed {path} under key {} ({tf})", kc.pack_u32()))
+            } else {
+                let (_, envelope) = store
+                    .get_record(&coord)
+                    .ok_or_else(|| format!("open: no record at {path}"))?;
+                let pt = env
+                    .open(store, Selector::Slot(0), &envelope)
+                    .map_err(|e| format!("open: {e:?}"))?;
+                let cell = CodeCell::from_record(coord, &CubeHeader::new(), &pt)
+                    .ok_or_else(|| "open: decrypted body is not valid bytecode".to_string())?;
+                // The VM runs code located by coordinate, so to execute a sealed
+                // record we decrypt it back into a plaintext record, then run.
+                store.put_record(coord, &CubeHeader::new(), &pt);
+                let mut vm = Vm::new(store.clone());
+                let res = vm.run(cell.label);
+                Ok(format!(
+                    "open+run {path} (key {}) => {res:?}",
+                    kc.pack_u32()
+                ))
+            }
+        }
+        other => Err(format!("unknown command: {other}")),
+    }
+}
+
+/// Parse a byte token: decimal (`42`) or hex (`0x2a`).
+fn parse_byte(t: &str) -> Option<u8> {
+    if let Ok(v) = t.parse::<u8>() {
+        return Some(v);
+    }
+    u8::from_str_radix(t.trim_start_matches("0x"), 16).ok()
+}
+
+/// Parse a coordinate `C.Z.Y.X` (decimal, allows 0 for Null space).
+fn parse_coord(s: &str) -> Option<cubecoords::Czyx> {
+    let parts: Vec<&str> = s.split('.').collect();
+    if parts.len() != 4 {
+        return None;
+    }
+    let nums: Option<Vec<u8>> = parts.iter().map(|p| p.parse::<u8>().ok()).collect();
+    let nums = nums?;
+    Some(cubecoords::Czyx::new(nums[0], nums[1], nums[2], nums[3]))
+}
+
+/// Parse a cubevm op name (case-insensitive) into an [`Op`]. `arg` is the
+/// operand byte for ops that take one (const/load/store/jmp/jz/jnz/call/ret/
+/// syscall); it is ignored for argument-less ops.
+fn make_op(t: &str, arg: u8) -> Result<Op, String> {
+    Ok(match t.to_ascii_lowercase().as_str() {
+        "nop" => Op::Nop,
+        "halt" => Op::Halt,
+        "const" => Op::Const(arg),
+        "load" => Op::Load(arg),
+        "store" => Op::Store(arg),
+        "add" => Op::Add,
+        "sub" => Op::Sub,
+        "mul" => Op::Mul,
+        "div" => Op::Div,
+        "mod" => Op::Mod,
+        "and" => Op::And,
+        "or" => Op::Or,
+        "xor" => Op::Xor,
+        "shl" => Op::Shl,
+        "shr" => Op::Shr,
+        "eq" => Op::Eq,
+        "ne" => Op::Ne,
+        "lt" => Op::Lt,
+        "gt" => Op::Gt,
+        "le" => Op::Le,
+        "ge" => Op::Ge,
+        "jmp" => Op::Jmp(arg),
+        "jz" => Op::Jz(arg),
+        "jnz" => Op::Jnz(arg),
+        "call" => Op::CallLink(arg),
+        "ret" => Op::Ret,
+        "syscall" => Op::Syscall(arg),
+        other => return Err(format!("prog: unknown op {other}")),
+    })
+}
+
+/// True for ops that consume the next token as a u8 operand.
+fn takes_arg(t: &str) -> bool {
+    matches!(
+        t.to_ascii_lowercase().as_str(),
+        "const" | "load" | "store" | "jmp" | "jz" | "jnz" | "call" | "syscall"
+    )
+}
+
+fn parse_transform(s: &str) -> Option<TransformId> {
+    match s {
+        "none" => Some(TransformId::None),
+        "gcm" => Some(TransformId::Aes256Gcm),
+        "chacha" => Some(TransformId::ChaCha20Poly1305),
+        "xts" => Some(TransformId::Aes256Xts),
+        _ => None,
+    }
+}

cubesys/src/bin/cube_demo.rs

@@ -0,0 +1,5 @@
+//! `cube-demo` binary: runs the shared integration demo (see `cubesys::demo`).
+
+fn main() {
+    cubesys::demo::run();
+}

cubesys/src/lib.rs

@@ -0,0 +1,371 @@
+//! CUBELinux-2 system integration — Packages 3-5 bound into one running
+//! system over a single [`CubeStore`] (PDF Packages 3-5).
+//!
+//! The five crates in CUBELinux-2 are deliberately separable. This crate is
+//! the composition layer the PDF implies but never names as a "Package 6":
+//! it proves the packages interoperate over a *shared* store, exactly as the
+//! original design intends ("data addressed by coordinate not path").
+//!
+//! The binding it enforces:
+//!
+//! * **cubefs** lays a POSIX namespace over the cube. Files live at
+//!   `C/Z/Y/X` paths; each file/record owns a [`Czyx`] coordinate.
+//! * **cubecode** stores code cells *as records* in the very same cube — so a
+//!   file path and a code cell address are the same coordinate. A function
+//!   written through cubefs at `/c012/z000/y000/x021` IS the cell the VM runs
+//!   at `Czyx::new(12,0,0,21)`.
+//! * **cubecrypt** seals records under a [`CubeEnv`]: the key material lives
+//!   in Null cubes of the *same* store, so the same coordinate opens to
+//!   different plaintext under a different environment.
+//!
+//! Two primitives tie them together:
+//!
+//! * [`load_code_cell`] — given a cubefs path, read that record and decode it
+//!   into a [`cubecode::CodeCell`]. This is the path→code bridge: a user
+//!   drops a `.fn` file, the VM runs it, no coordinate bookkeeping required.
+//! * [`path_to_czyx`] — the single bijection (re-exported from `cubefs`) so
+//!   every layer agrees on where a path lands in the cube.
+//!
+//! The big design decision (documented in `docs/integration.md`): the cube is
+//! the single source of truth. cubefs is a *view* of the cube, cubecode is a
+//! *kind* of record in it, and cubecrypt is a *transform* applied to records
+//! in it. None of them own storage; the store does. That is the whole point of
+//! "coordinate-addressed" — and it is what this crate makes runnable.
+
+#![forbid(unsafe_code)]
+#![warn(missing_docs)]
+
+use cubecode::{CodeCell, Kind};
+use cubecoords::{CubeHeader, Czyx};
+use cubefs::path::parse_path;
+use cubestore::{CubeBackend, CubeStore, HashBackend};
+
+/// The error type for system-level operations that span packages.
+#[derive(Clone, Eq, PartialEq, Debug)]
+pub enum SysError {
+    /// The path did not parse as a cube path.
+    BadPath(String),
+    /// No record exists at the resolved coordinate (plain or encrypted).
+    MissingRecord(Czyx),
+    /// The record's body is not valid cubevm bytecode.
+    NotCode(Czyx),
+    /// The cubecrypt envelope failed to open (wrong env / tampered / bad
+    /// magic). Carries a human reason.
+    Crypto(String),
+}
+
+impl std::fmt::Display for SysError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            SysError::BadPath(s) => write!(f, "bad path: {s}"),
+            SysError::MissingRecord(c) => {
+                write!(f, "no record at coord {}", c.pack_u32())
+            }
+            SysError::NotCode(c) => {
+                write!(f, "record at coord {} is not valid bytecode", c.pack_u32())
+            }
+            SysError::Crypto(s) => write!(f, "crypto error: {s}"),
+        }
+    }
+}
+
+/// Resolve a POSIX path to its [`Czyx`] coordinate using the cubefs bijection.
+///
+/// This is the canonical entry point every layer should use so path and
+/// coordinate never disagree. `c000` and friends are rejected (Null space is
+/// not a path), so a returned coordinate is always a user-addressable record
+/// or directory prefix.
+pub fn path_to_czyx(path: &str) -> Result<Czyx, SysError> {
+    let parsed = parse_path(path).map_err(|e| SysError::BadPath(e.to_string()))?;
+    parsed
+        .czyx()
+        .ok_or_else(|| SysError::BadPath(format!("{path:?} names a directory, not a record")))
+}
+
+/// Load (and decode) the code cell stored at a cubefs file path.
+///
+/// This is the bridge that makes "a file is a function" literally true: it
+/// reads the record at the path's coordinate through the *same* store cubefs
+/// uses, then decodes the body as cubevm bytecode via [`cubecode`]. Returns the
+/// typed [`CodeCell`] so callers get the kind, name, links and decoded ops.
+pub fn load_code_cell<B: CubeBackend>(
+    store: &CubeStore<B>,
+    path: &str,
+) -> Result<CodeCell, SysError> {
+    let coord = path_to_czyx(path)?;
+    let (header, body) = store
+        .get_record(&coord)
+        .ok_or(SysError::MissingRecord(coord))?;
+    // Prefer a code cell if the record carries a code doc_type; otherwise try
+    // to decode whatever is there (the cube is code-as-data, so a raw record
+    // body may still be valid bytecode).
+    if let Some(cell) = CodeCell::from_record(coord, &header, &body) {
+        Ok(cell)
+    } else {
+        Err(SysError::NotCode(coord))
+    }
+}
+
+/// Build a [`CodeCell`] from parts and write it back as a record at `path`,
+/// so code written by the VM (or tooling) is visible to cubefs at that path.
+pub fn store_code_cell<B: CubeBackend>(
+    store: &mut CubeStore<B>,
+    path: &str,
+    kind: Kind,
+    name: &str,
+    links: &[Czyx],
+    code: &[cubecode::Op],
+) -> Result<Czyx, SysError> {
+    let coord = path_to_czyx(path)?;
+    let mut h = CubeHeader::new();
+    h.title = Some(name.to_string());
+    h.doc_type = Some(kind.as_str().to_string());
+    h.linked_records = links.to_vec();
+    if h.doc_type.as_deref() == Some("fn") {
+        h.size_bytes = Some(cubecode::encode(code).len() as u64);
+    }
+    h.refresh_flags();
+    store.put_record(coord, &h, &cubecode::encode(code));
+    Ok(coord)
+}
+
+/// Convenience: an in-memory system store, the default for demos/tests.
+pub fn memory_store() -> CubeStore<HashBackend> {
+    CubeStore::new(HashBackend::new())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use cubecode::Op;
+    use cubecoords::Czyx;
+    use cubecrypt::{CubeEnv, KeySlot, Selector, TransformId, HEADER_FLAG_ENCRYPTED};
+
+    #[test]
+    fn path_is_the_code_cell_coordinate() {
+        // The headline property: a cubefs path and a code cell resolve to the
+        // SAME coordinate, so the VM runs what cubefs lists as a file.
+        // Note: axis value 0 is Null control space and is NOT a valid path
+        // component, so every axis here is non-zero.
+        let coord = path_to_czyx("/c012/z001/y001/x021").unwrap();
+        assert_eq!(coord, Czyx::new(12, 1, 1, 21));
+
+        let mut store = memory_store();
+        let path = "/c012/z001/y001/x021";
+        store_code_cell(
+            &mut store,
+            path,
+            Kind::Fn,
+            "add",
+            &[],
+            &[Op::Const(2), Op::Const(3), Op::Add, Op::Halt],
+        )
+        .unwrap();
+
+        // cubefs sees it as a file at that path...
+        let fs = cubefs::CubeFs::new(store.clone());
+        assert_eq!(fs.kind_of(path).unwrap(), cubefs::Kind::File);
+
+        // ...and cubecode decodes the very same record as a runnable cell.
+        let cell = load_code_cell(&store, path).unwrap();
+        assert_eq!(cell.kind(), Kind::Fn);
+        assert_eq!(cell.name(), Some("add"));
+        assert_eq!(
+            cell.code,
+            vec![Op::Const(2), Op::Const(3), Op::Add, Op::Halt]
+        );
+
+        // run it through the VM on the shared store
+        let mut vm = cubecode::Vm::new(store.clone());
+        assert_eq!(vm.run(coord), cubecode::RunResult::Halted { top: Some(5) });
+    }
+
+    #[test]
+    fn encrypt_then_run_is_the_same_record() {
+        // Encrypt a record via cubecrypt, confirm the same coordinate now
+        // carries an encrypted body, then decrypt and run it.
+        let mut store = memory_store();
+        let env = CubeEnv::new(
+            vec![KeySlot {
+                key_cell: Czyx::new(0, 1, 0, 1), // Null cube 1
+                transform: TransformId::Aes256Gcm,
+                salt: vec![],
+            }],
+            vec![],
+        );
+        store.put_record(
+            Czyx::new(0, 1, 0, 1),
+            &CubeHeader::new(),
+            b"environment-root-key-32bytes!!",
+        );
+
+        let coord = path_to_czyx("/c005/z001/y001/x007").unwrap();
+        // plaintext bytecode first
+        let code = vec![Op::Const(7), Op::Halt];
+        store.put_record(coord, &plaintext_header(), &cubecode::encode(&code));
+        assert!(load_code_cell(&store, "/c005/z001/y001/x007").is_ok());
+
+        // now seal the SAME coordinate under the env
+        env.put_encrypted(
+            &mut store,
+            coord,
+            Selector::Slot(0),
+            &cubecode::encode(&code),
+            CubeHeader::new(),
+        )
+        .unwrap();
+        let (h, _body) = store.get_record(&coord).unwrap();
+        assert!(h.flags.has(HEADER_FLAG_ENCRYPTED));
+        // the raw record body is no longer plaintext bytecode
+        assert!(load_code_cell(&store, "/c005/z001/y001/x007").is_err());
+
+        // decrypt + decode + run on the shared store
+        let envelope = store.get_record(&coord).unwrap().1;
+        let pt = env.open(&store, Selector::Slot(0), &envelope).unwrap();
+        let cell = CodeCell::from_record(coord, &CubeHeader::new(), &pt).unwrap();
+        assert_eq!(cell.code, code);
+        // The VM runs code located by coordinate, so to *execute* a sealed
+        // record we decrypt it back into a plaintext record at the same coord,
+        // then run. (Reading the encrypted envelope directly would fail decode.)
+        store.put_record(coord, &CubeHeader::new(), &pt);
+        let mut vm = cubecode::Vm::new(store.clone());
+        assert_eq!(vm.run(coord), cubecode::RunResult::Halted { top: Some(7) });
+    }
+
+    fn plaintext_header() -> CubeHeader {
+        let mut h = CubeHeader::new();
+        h.doc_type = Some("fn".into());
+        h.refresh_flags();
+        h
+    }
+}
+
+/// The integration demo: build ONE in-memory [`CubeStore`] and run cubefs,
+/// cubecode and cubecrypt over it, printing evidence at each step.
+///
+/// See `docs/integration.md`. Shared by the `cube` and `cube-demo` binaries.
+pub mod demo {
+    use cubecode::{Kind, Op, Vm};
+    use cubecoords::Czyx;
+    use cubecrypt::{CubeEnv, KeySlot, Selector, TransformId};
+    use cubestore::{CubeStore, HashBackend};
+
+    /// Run the integration tour.
+    pub fn run() {
+        println!("=== CUBELinux-2 integration demo ===\n");
+
+        let mut store = CubeStore::new(HashBackend::new());
+
+        // ---- 1. write code cells as cubefs paths, run through the VM ----------
+        println!("[1] cubefs + cubecode: a path IS a code cell");
+        let double = "/c002/z001/y001/x001";
+        let entry = "/c001/z001/y001/x001";
+
+        let double_code = vec![Op::Store(0), Op::Load(0), Op::Const(2), Op::Mul, Op::Ret];
+        let entry_code = vec![Op::Const(21), Op::CallLink(0), Op::Halt];
+
+        let double_coord =
+            super::store_code_cell(&mut store, double, Kind::Fn, "double", &[], &double_code)
+                .expect("store double");
+        let entry_coord = super::store_code_cell(
+            &mut store,
+            entry,
+            Kind::Fn,
+            "entry",
+            &[double_coord],
+            &entry_code,
+        )
+        .expect("store entry");
+        println!("  wrote {double}  -> coord {}", double_coord.pack_u32());
+        println!("  wrote {entry}  -> coord {}", entry_coord.pack_u32());
+        println!(
+            "  entry links to double at coord {}",
+            double_coord.pack_u32()
+        );
+
+        // cubefs sees both as files in the same cube
+        let fs = cubefs::CubeFs::new(store.clone());
+        let root = fs.readdir("/").expect("readdir /");
+        println!(
+            "  cubefs '/' lists: {}",
+            root.iter()
+                .map(|(n, _)| n.clone())
+                .collect::<Vec<_>>()
+                .join(" ")
+        );
+
+        // load the entry cell the same way the CLI would, and run it
+        let cell = super::load_code_cell(&store, entry).expect("load entry");
+        let mut vm = Vm::new(store.clone());
+        let res = vm.run(cell.label);
+        println!("  VM ran {entry}: {res:?}  (expected Halted 42)");
+        assert_eq!(res, cubecode::RunResult::Halted { top: Some(42) });
+
+        // ---- 2. cubecrypt: seal a record, then open + run it -----------------
+        println!("\n[2] cubecrypt: same coordinate, sealed + reopened");
+        // Key material lives in Null space (axis value 0) — not a cubefs path.
+        let key_cell = Czyx::new(0, 1, 0, 1);
+        store.put_record(
+            key_cell,
+            &cubecoords::CubeHeader::new(),
+            b"demo-key-material-32-bytes-long!!",
+        );
+        let env = CubeEnv::new(
+            vec![KeySlot {
+                key_cell,
+                transform: TransformId::Aes256Gcm,
+                salt: vec![],
+            }],
+            vec![],
+        );
+
+        let sealed = "/c003/z001/y001/x005";
+        let sealed_coord = super::path_to_czyx(sealed).expect("parse sealed path");
+        // store plaintext bytecode, then seal the same coordinate
+        store.put_record(
+            sealed_coord,
+            &cubecoords::CubeHeader::new(),
+            &cubecode::encode(&[Op::Const(9), Op::Halt]),
+        );
+        env.put_encrypted(
+            &mut store,
+            sealed_coord,
+            Selector::Slot(0),
+            &cubecode::encode(&[Op::Const(9), Op::Halt]),
+            cubecoords::CubeHeader::new(),
+        )
+        .expect("seal");
+        let (h, _) = store.get_record(&sealed_coord).expect("read sealed");
+        println!(
+            "  sealed {sealed}: header encrypted flag set = {}",
+            h.flags.has(cubecrypt::HEADER_FLAG_ENCRYPTED)
+        );
+
+        // the raw record is no longer readable as plaintext bytecode
+        let raw = store.get_record(&sealed_coord).unwrap().1;
+        let still_plain =
+            cubecode::CodeCell::from_record(sealed_coord, &cubecoords::CubeHeader::new(), &raw);
+        println!(
+            "  raw record decodes as bytecode? {}",
+            still_plain.is_some()
+        );
+
+        // open + decode + run on the shared store. The VM runs code located by
+        // coordinate, so to *execute* the sealed record we decrypt it back into a
+        // plaintext record at the same coord, then run.
+        let envelope = store.get_record(&sealed_coord).unwrap().1;
+        let pt = env
+            .open(&store, Selector::Slot(0), &envelope)
+            .expect("open");
+        let opened =
+            cubecode::CodeCell::from_record(sealed_coord, &cubecoords::CubeHeader::new(), &pt)
+                .expect("decode decrypted bytecode");
+        store.put_record(sealed_coord, &cubecoords::CubeHeader::new(), &pt);
+        let mut vm2 = Vm::new(store.clone());
+        let res2 = vm2.run(opened.label);
+        println!("  opened + ran {sealed}: {res2:?}  (expected Halted 9)");
+        assert_eq!(res2, cubecode::RunResult::Halted { top: Some(9) });
+
+        println!("\n=== demo OK: one cube, three packages, same coordinates ===");
+    }
+}