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Governed package installation for kernels - #281

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KB (KB-syntheticsciences) wants to merge 49 commits into
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feat/kernel-package-install
Draft

Governed package installation for kernels#281
KB (KB-syntheticsciences) wants to merge 49 commits into
mainfrom
feat/kernel-package-install

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What does this PR do?

Gives the agent a governed way to install packages — and closes the only ungoverned way.

A new package_install tool installs into named, language-scoped environments behind an approval
card. Kernels bind to an environment through an environment parameter beside kernel, and an
install restarts them only when the change is not purely additive. Shell installers are refused
before they run.

Stacked on #280 (bounded network egress); merge that first.

What a user gets

before after
Agent installs a package no mechanism at all package_install, one approval card
Approval scope install tqdm → default [pypi.org/simple], with a standing install* grant
pip install in the agent shell silently succeeds, ungoverned refused, naming the tool
Where packages land host site-packages (read-only) or nowhere a managed per-project environment
Kernel after an additive install keeps its variables
Kernel after an upgrade/removal restarted, because a loaded module would be silently stale
R no mechanism install.packages into R_LIBS_USER

Why the refusal is part of this PR, not a follow-up

#280 made shell installs work. Measured on that branch, inside the agent's own sandbox, with no
tool and no card:

python3 -m venv <workspace>/venv && <workspace>/venv/bin/pip install tqdm   →  4.70.0

The workspace is writable and pypi is allowlisted, so read-only system site-packages stops nothing.
Before the proxy this died at DNS and the install contract held by accident; the proxy removed the
accident, not the intent. An approval card that an agent can walk around is decorative, so the
refusal and the tool ship together and are asserted in the same test.

It is a contract boundary, not a security boundary — the same egress can fetch a wheel by hand —
and the code says so rather than claiming more.

How did you verify your code works?

By running it. Six defects were found by tests the plan did not call for, every one invisible to the
suite as planned:

  • uv venv does not install pip. The ladder prefers uv, but install() shells out to
    python -m pip, so on any machine with uv it produced an environment the installer could not use.
    Every other test passed, because the one asserting "a venv has pip" forces the venv branch. Fixed
    with uv venv --seed.
  • A manifest that could never be read back. execute is reachable without zod defaults applied,
    so language was undefined, JSON.stringify dropped the key, and read's parse rejected the
    file. The environment existed on disk with packages in it and was invisible to the inventory.
    Environment.write now validates before writing.
  • The kernel could not see its environment. "No such file or directory" for an interpreter that
    exists. Production would have worked by luck (~/.cache is under --ro-bind / /); --tmpfs /tmp
    masks it wherever the cache root lives under /tmp.
  • wrapArgv discarded policy.readBind at two call sites, replacing it wholesale with the
    egress shim's paths. The environment bind was dropped on the floor with no error.
  • six==1.17.0 over an installed 1.16.0 reported "already installed". The skip check compared
    names only, so an upgrade became a silent no-op that also reported the change as additive —
    leaving the old version in place while telling the agent it had the new one.
  • token() is undefined on Windows. The plan's reconcile rule would have marked every Windows
    install unknown forever and every environment permanently suspect.

Also fixed npm pack --json, which returns an object on npm 12 and an array before it — the test
indexed [0], so it failed on any current npm while passing on CI's older one.

  • bun run typecheck passes
  • bun test (in backend/cli) — 2111 pass / 6 skip / 0 fail
  • bunx prettier --check . clean
  • Linked an issue
  • Screenshots — the approval card is new UI worth a look

Merge gate

test/package/install-live.test.ts states the condition as an assertion, and the CI sandbox job runs
test/package/ on both legs so it is a fact on each platform rather than a claim about one:

pip under allowlist user approval
Linux ✅ live in CI ✅ live in CI
macOS ✅ (pending this PR's first run) ✅ (pending this PR's first run)
Windows Sandbox.backend() is "none"

Windows still blocks the gate, exactly as before this PR: kernels do not run there at all, so the
suite skips rather than fails. It needs the AppContainer + broker design in
docs/specs/windows-sandbox-design.md.

Known gaps, stated rather than hidden

  • R's CRAN round trip is unverified. Rscript is not installed on the development machine, so
    the two live R tests skip. Everything else about the R path — the explicit lib, the
    warning-not-exit-code failure check, the message translation — is tested.
  • pip's cache is disabled inside the sandbox, so every install re-downloads. Correct behaviour
    for a read-only /, real repeat cost across a session. Whether to bind a writable per-project
    cache is a deliberate open decision.
  • The wait: false path has no notification channel; a later call is how the agent learns the
    outcome, and the tool's output says so rather than implying otherwise.

Binary network is the wrong granularity: deny locks kernels out of PyPI
and the scientific APIs, allow is unrestricted egress. A spike
established an enforceable middle — --unshare-net blocks every host
including the host's own loopback, while a bind-mounted unix socket
still crosses the namespace, so the socket is the only route out and the
proxy decides what is reachable.

Recorded before implementation because it is a breaking change to a
documented config key, and because it deletes the separate install
sandbox rather than adding a component.
The mechanism paragraph quotes two measured values from the spike; three
other statements were the ADR's own forward decisions but read in the
same flat register, so a reader couldn't tell which was which. Rewords
those three to say plainly that they are decisions this record is
taking, and marks the seatbelt warning behaviour as unverified rather
than stating it as settled fact.

No content removed — the brief's ten required points all still appear.
Ported from the spike on proto/sandbox-allowlist-proxy. The matcher is
pure and separable so the allowlist is testable without sockets.

Both measured fixes carried across: the shim buffers writes arriving
before the upstream unix connection resolves, and the proxy rewrites
absolute-form to origin-form for plain HTTP.
allowlist keeps --unshare-net and binds a unix socket as the only route
out, so the proxy on the far end is enforcement rather than advice. The
builder refuses allowlist without a socket path instead of silently
producing an open sandbox.

Seatbelt has no namespace equivalent, so it reads allowlist as deny:
falling back to allow would grant unrestricted egress to a user who
asked for a bounded one.
…ments

buildPolicy now filters `egress` through the same tooBroadToConfine gate
as writable/unreadable. An over-broad egress (e.g. $HOME, "/") was
reaching bubblewrapArgs unfiltered and becoming a read-write --bind,
defeating write containment entirely. A rejected path is dropped, which
leaves "allowlist" without an egress socket, so bubblewrapArgs' existing
missing-egress check still throws — fails closed either way.

Also corrects two comments that asserted things that weren't true: the
--bind comment overstated the socket bind as the access-control
mechanism (unshare-net is; the bind only makes the path reachable), and
plan()'s doc comment no longer mentioned the allowlist-without-egress
throw it gained in the previous change.
…heck

The round-1 fix checked tooBroadToConfine against the raw egress string,
so a trailing slash, a double slash, or an unresolved ".." bypassed the
gate entirely (strict string equality never matched) while resolving to
the exact same over-broad path on disk. writable/unreadable were never
vulnerable to this because they already went through dedupe()'s
path.resolve() before the same check. Route egress through the same
dedupe() call instead of hand-rolling separate normalization, so the
two paths cannot drift apart again.

Test coverage widened from the one literal string to the class of
lexical variants (trailing slash, double slash, unresolved ..), plus a
control asserting a legitimate non-broad socket still gets bound.
pip, requests and curl take a host:port proxy and none speak unix
sockets, so a loopback listener inside the namespace bridges to the
bind-mounted socket. It runs from the OpenScience binary, which is
already visible under --ro-bind / /, so nothing extra ships.

Script composition is a pure function with quoting tests, because a path
with a space or a quote in agent-authored code would otherwise split the
command.
…turally

Two live-verified breaks in the composed egress shim:

The shim went through yargs' global middleware before reaching its
handler, which opens a log file (EROFS under the sandbox's read-only
root) and fetches over HTTP (hangs under --unshare-net). shimScript
redirected the shim's own output to /dev/null, so this failed
completely silently: network "allowlist" behaved exactly like deny.
Handle __egress-shim as a raw argv check before any yargs construction
so it can never reach the middleware, regardless of what middleware
grows there later.

The dev-mode launcher resolved its target script from Bun.main, which
is whatever launched the current process. Under bun test that's the
test file, not the CLI entry - the exact context Task 6's live test
runs under. Resolve the entry from sandbox.ts's own location instead,
a structural relationship unaffected by what invoked the process.

Fixing that surfaced a second issue: the launcher's content-addressed
cache location under Global.Path.state resolved under the OS tmp dir
during bun test (test isolation redirects every XDG dir there), and
bubblewrapArgs unconditionally mounts a fresh tmpfs over /tmp inside
the sandbox - so the launcher silently didn't exist from inside and
the shim never started. Anchored the launcher to the repo checkout
itself instead, which neither test nor a real user's env can redirect.

Also added a bounded marker-file readiness wait before exec, since the
real command was exec'd immediately and anything doing network I/O in
the shim's ~600ms startup window got connection-refused.
…location

Location-based fixes for --tmpfs /tmp masking (Global.Path.state, then the
launcher's own checkout directory) both re-anchored the same bug instead of
removing it: a real checkout under /tmp (git worktree add /tmp/..., a CI
mktemp -d clone, a container build) masks the launcher exactly like an
XDG dir redirected under os.tmpdir() during bun test does. There is no
location immune to both. Bind the launcher back in explicitly after
--tmpfs /tmp instead, the same way the egress socket already is
(--ro-bind-try, read-only: it's executed, never written to, from inside).
Policy gains readBind for this; the launcher lives in Global.Path.bin
again, matching ensureAtlasBinDir, purely for tidiness now that its
location no longer needs to be "safe."

Split the dev-mode launcher's target off of src/index.ts into a new
minimal entry (egress-shim-entry.ts) that imports only Egress.serveShim.
index.ts's full graph pulls in Global's unguarded top-level cache-version
write (EROFS under a read-only tree) and a live models.dev fetch, both
reachable before any argv check could skip them - live-reproduced with a
stale/read-only cache dir. A compiled binary has no separate entry to
redirect to, so it still evaluates that graph; documented as a residual
in the Task 4 report rather than restructuring index.ts's ~30 command
imports into dynamic ones.

Also: the readiness wait now sleeps in whole seconds, since fractional
sleep is a coreutils extension busybox doesn't reliably support and a
rejected sleep would skip the wait entirely instead of slowing it down;
and the live sandbox-execution test resolves bash from the same
Bun.which() gate it skips on, instead of hardcoding /usr/bin/bash, so it
skips rather than fails on Alpine/non-usrmerge Debian.
…verlaps

Two more instances of the /tmp-masking class, both live-reproduced:

The dev bind list covered the launcher and the package root but not the
interpreter the launcher's exec line names (process.execPath) - it can
itself live under /tmp (a portable bun install, $HOME under /tmp),
independent of where the launcher or checkout live. Reproduced with a
bun binary staged under /tmp: byte-identical failure signature to the
original bug. Now bound alongside the other two.

bubblewrapArgs emits readBind after the writable --bind-try loop, so a
later read-only mount at (or inside) an already-writable path shadows
it. With a workspace that is or contains this package's own checkout -
the self-hosting case Task 5 will dogfood - binding the package root
read-only turned src/sandbox back read-only despite being nominally
writable. Fixed by excluding any readBind path already covered by an
actually-bound writable root before emitting it. "/tmp" itself needed
special handling: it is always nominally writable (tempDirs() adds it
unconditionally) but is deliberately never bound - the fresh tmpfs
already provides it - so treating it as "covers everything under it"
reintroduced the original masking bug for a launcher that resolves
under /tmp during bun test. Caught by the existing live test before
this ever left the working tree.

Only one containment direction is guarded (a readBind path inside a
writable root); the reverse has no realistic trigger given today's
three readBind candidates and would need reordering these mounts to
handle, risking the same shadowing bug in the other direction.

Consolidated the readiness-marker literal, previously duplicated across
three files and kept in sync by comment only, into one exported
constant all three import.

Added regression coverage for both: the live test parametrized over an
interpreter staged under /tmp (stages a real bun copy, drives a
standalone script through it - bun:test itself isn't the thing under
test), and a write-probe under a workspace that overlaps the package
root. Both have negative controls confirming they fail without their
respective fix.
…disk

The shim's launcher exec'd bun against egress-shim-entry.ts, so every path
bun touched resolving that source had to be bound back past --tmpfs /tmp.
Four revisions bound the paths their author thought of and each missed one.
The last: in this bun workspace an npm import resolves through
backend/cli/node_modules/<pkg>, a symlink into the monorepo-root store one
level above the package root, so binding the package root bound the link and
not its target. Reproduced against a /tmp-relocated checkout with a real
hoisted store — one added import turned the shim into ENOENT, connection
refused, silent.

Build the entry into a self-contained bundle instead and exec that: at run
time bun opens one file, so the bound set is closed by construction — the
launcher, the bundle, the interpreter — rather than a list that has to keep
pace with an import graph. bun build costs 3ms, once per process, on the
allowlist path only, and fails loudly at wrapArgv time. The artifacts are
content-addressed and renamed into place, so a rebuild cannot overwrite one
another process is executing and a stale launcher/bundle pair cannot form.

That drops the package root from readBind, which also removes the shadowing
hazard the writable-overlap exclusion guards: every remaining path is a
regular file, so nothing can nest inside one. The old justification for
guarding only that direction claimed no workspace would sit under those
locations, which is not true — write roots also come from session grants and
allowWrite — so it now gives the reason that holds.

Two tests, neither needing the relocated-checkout fixture: the generated
bundle carries no import specifier but builtins, and the shim still bridges
with its own source entry masked to /dev/null.
…ltin list

bun build strips the node: prefix, so a bundled `import "node:net"` reaches
the guard as `from "net"` and the prefix filter flagged it — a false alarm on
the next honest edit, aimed at the one check that closes the npm-import class.
The same filter excused any package named bun-something, and its regex never
matched a bare side-effect `import "x"` at all. Ask builtinModules instead,
after stripping node:; it already carries bun's own entries. Measured on real
bundles: net passes, diff / bun-pty / fuzzysort are all flagged.

Two doc corrections alongside it. The bundle digest also varies with the
process cwd, since bun build writes cwd-relative module banners — that is the
dimension that actually varies per invocation. And the residual list was
missing a fourth entry: a dependency loading a native binding bundles cleanly
and still dlopens a .so at run time, which is not an import specifier and so
is invisible to both the reasoning and the guard.
One proxy per process, held in a lazily-created singleton with a
disposer (not Instance.state: a global config write disposes every open
instance, and the proxy must outlive that or every kernel bound to its
socket loses its only route out). Socket lives under the state
directory.

Rules are read per connection rather than captured at start: refreshed
on every ensure() and reactively on global config changes via GlobalBus,
so editing the allowlist takes effect without tearing down kernels -
which is why proxy policy stays out of the generation hash.

sandbox.network defaults to allowlist. Both cases of the proxy
variables reach kernels: curl reads lowercase http_proxy and ignores
the uppercase form for HTTP. Widened three downstream network enums
(execution authority, sandbox settings route, persisted job records)
plus a fourth (KernelEnvironment) surfaced by typecheck. Exported
Sandbox.SHIM_PORT so EgressRuntime.ensure() returns the same port
sandbox.ts already uses, instead of a second constant that could drift.
network defaulting to allowlist exposed that no caller of Sandbox.wrapArgv
supplied the egress socket bubblewrapArgs requires for that policy, so
every sandboxed kernel, terminal, and compute job spawn threw instead of
running. Sandbox.plan() (the bash tool's path) never composed a shim at
all, so pip/curl/uv - the feature's motivating case - had zero network
under allowlist regardless.

EgressRuntime.egressFor(policy) is the single decision point: it starts
the proxy only when it would actually be used (bubblewrap backend,
network "allowlist"), so a terminal on macOS or under network "deny"
never pays for a proxy it has no way to reach. Every wrapArgv caller
(notebook/rkernel/biology kernels, compute jobs x4, pty terminals) and
bash.ts's plan() call now route through it and merge the returned
Wrapped/Plan.env into the spawned process's environment, which had been
an unconsumed seam since Task 4.

Sandbox.plan() now composes the same loopback shim wrapArgv does, for a
shell -c command instead of a file/args pair, by feeding shimScript the
shell invocation as its argv - one composition, not two.

Widened two test files' stale "deny"-only assertions to allow the new
allowlist default, widened five notebook-test/command-runtime polling
budgets that were tuned for pre-shim startup latency (the shim's own
wait can take up to ~3s), and made one shell.test.ts assertion filter
by pid instead of assuming absolute call order on a process-wide
process.kill mock - a race that was always latent but only became
probable once real sandboxed spawns became this common in the suite.

Full suite: 74 failures -> 1 (an npm-pack environment flake confirmed
present on the pre-Task-5 baseline too, unrelated to this branch).
…wn latency

Three live-verified Criticals on the egress path.

Backpressure. Both bridges called Socket.write and discarded the byte count
it returns, with no drain handler on either side, so every transfer past one
kernel send buffer lost its tail: 40 MB arrived as 2.8 MB through the proxy
and 11.6 MB through shim + proxy, and pypi.org/simple/ (44,841,256 bytes)
came back as 4.7/10.8/5.6 MB with "bad record mac" from curl. A pump per
direction now queues what the destination refused, flushes from that
destination's drain, pauses the source while a backlog exists, and defers
end() until the queue has gone out. All three sizes now arrive byte-exact.

Latched start. EgressRuntime cached the start promise unconditionally, so one
transient failure was replayed to every later caller for the process
lifetime, and stop() re-raised it instead of clearing it. Under the allowlist
default that is every bash command, terminal, kernel and compute job broken
until restart. A rejected start now un-caches itself, stop() is safe after
one, and the bind failure carries a message naming what depends on it.
Callers still throw rather than degrade: silently downgrading to no-proxy is
the failure this feature keeps producing.

Spawn latency. shimScript polled for readiness at whole-second granularity
while the bundled shim binds in ~12 ms, so every sandboxed spawn paid a flat
second whether or not it touched the network -- n=8, 1006 ms against 3 ms for
network "deny". The interval is now settled once by a single fractional sleep
whose stderr is discarded, falling back to whole seconds where busybox
rejects it; same 3s cap either way. Same measurement: 26 ms.

Regression tests move real volume (8 MB, both directions, byte-exact), drive
a real start failure, and time the composed script through a real /bin/sh.
Each fails against the code it fixes.
Both bridges dial from inside an async handler, and Bun does not serialize
those handlers -- a second chunk, or a client's FIN, re-enters while the first
call is parked on await Bun.connect. Two defects lived in that window.

An aborted connection stranded a socket at both ends. A client whose FIN
lands before Bun.connect(unix) resolves has its close handler run while there
is no link yet, so it tears down nothing, and the socket the dial then
produces is owned by nobody -- which also pins the host proxy's accepted
connection. Measured across three processes, 300 connect-then-close
connections leaked 0.897 fd/conn in the shim and 0.897 in the host proxy;
now 0.000 in both, with completed connections unchanged at 0.000 throughout.
Bounded by the sandbox's lifetime, which for a kernel or terminal is hours.

One client produced several upstream dials. A body arriving after its head
re-entered data, found no link, re-parsed the same buffered head and dialled
again: 2 upstream connections against a local origin, 4 against a real
remote one, both carrying a duplicate of a non-idempotent request with the
body split between them. Reachable in practice -- wrapArgv sets HTTP_PROXY
too, and "a request with a body" is the shape NCBI E-utilities recommends
for large id lists, against a host in DEFAULT_RULES.

Both close on one four-state phase claimed synchronously before the await.
The body needs no second queue: everything before the link stays in the one
buffer already there, and rest is sliced after the dial rather than before,
so bytes that arrive during it go upstream in order by construction.

Three regression tests count sockets opened against sockets closed at a
stand-in upstream, so they measure the invariant without /proc. All three
fail against the code they fix, three runs out of three.
Both pre-link phases of the host proxy buffered without limit, and the
proxy runs in the CLI's own process — so a single sandboxed process could
exhaust, and then kill, its own supervisor.

  head     no dial is ever attempted on this path, so nothing bounded it.
           93 MiB of never-terminated head took the host process from
           36.0 MB to 1344.9 MB of RSS in 8 s, still climbing.
  dialing  a complete CONNECT to an allowlisted host that black-holes SYNs.
           2048.6 MiB blasted in 8 s took it from 36.0 MB to 2120.2 MB and
           then killed it with RangeError: Out of memory, dial still in
           flight and ~2 minutes of kernel SYN retries left to go.

The head gets a 64 KiB cap (Squid's request_header_max_size default, the
most generous of the conventional caps) and a 431. There is no
backpressure to apply there: the terminator is what the parse waits for,
so declining to read would deadlock rather than end the connection.

The dial window gets real backpressure instead of a cap — client.pause()
for as long as the dial is in flight, so the bytes stay in the client's
own buffer and there is no limit to tune. The previous round declined
this on the grounds that pausing would suppress the FIN that reports the
client leaving. Measured, it does not: with delivery demonstrably stopped
(0.21 MiB through a paused socket against 256 MiB unpaused), the peer's
end() still produced close while the pause was in force, for FIN and RST
alike. serveShim's identical window is paused for the same reason.

Dials also now time out at 30 s rather than riding the kernel's ~130 s
SYN-retry budget, answering 504 instead of hanging undiagnosably.

After, same measurements: head 36.0 -> 38.3 MB (+2.3), dial 36.0 -> 37.5
MB (+1.5) with the process alive and the client's own writes stalled.

Three regression tests, each failing against the parent commit: no
response at all for the head, 2,147,690,880 bytes accepted for the dial,
and no answer within 20 s for the timeout. Re-verified unchanged: 8 MB
byte-exact both directions through both bridges, flat RSS under a stalled
reader (origin stopped at 6.1 MiB, proxy +2.9 MB over 10 s), 0.000 fd/conn
across 600 aborts, one upstream dial per client, and a real bwrap fetch of
pypi.org/simple/ at 44,841,256 bytes matching the host's sha256 3/3 with
the deny control still returning 403.
…ss defaults

Four held-back findings from the task-5 review, fixed together:

- allowHosts was inert: the settings route PatchSchema silently dropped it
  (zod strips unknown keys) and the CLI never exposed it. Both now accept it,
  reaching the already-working reactive proxy reload.
- cli/cmd/sandbox.ts's `network` choices still only listed "allow"/"deny",
  so `--network allowlist` was rejected and a user on "deny" had no CLI path
  back to the new default; the `as "allow" | "deny"` cast that hid this from
  tsgo is gone along with it. Status/help text updated to match.
- egressFor() and decide()/buildPolicy() answered "what does a missing
  enabled/network mean" differently in both directions, invisible from
  today's five fully-resolved production callers but live for any other.
  Sandbox.resolved() is now the one place both read from, with a regression
  test pinning each direction.
- ExecutionAuthority.Decision.sandbox.network is a second copy of the
  persisted enum Job.sandbox.network carries (via Job.authority) — recorded
  where both schemas live, including that ComputeJobs.read() fails the whole
  job history file on one unparseable record, not just that record.

Verified past the type system: PUT to the settings route and `sandbox enable
--network allowlist --allow-host` each drive a real sandboxed curl through
to an allowed host and a 403 off a disallowed one, and each is shown to have
been impossible before this change (silently dropped field / rejected CLI
choice) in the same isolated run.
Asserts allowlisted hosts reach 200, denied hosts do not, and — the
load-bearing pair — that direct egress with the proxy unset fails and
getent resolves nothing. Without those two the test would prove the
proxy works, not that it is the only way out.

Skipped where bubblewrap or curl is absent rather than failing.
curl's own -m budget on the volume test matched the outer bun:test
timeout exactly, with bwrap spawn and shim-readiness overhead layered
on top before curl even starts. A slow-but-working download would hit
the outer timeout first, trading curl's own diagnostic for a generic
one and deferring the proxy's cleanup until the abandoned promise
resolves. Also strips ALL_PROXY/NO_PROXY (and lowercase) alongside the
existing HTTP(S)_PROXY vars in the direct-egress subshell, so a host
exporting ALL_PROXY can't route that check through an unrelated proxy.
…chmod it shut

The egress socket was bind-mounted read-write, and the bind shares the host
inode: a sandboxed process could discover the path via /proc/self/mountinfo
and `chmod 000` it, which persists on the host and disables egress for
every kernel/terminal/job sharing this one process-lifetime socket.
--ro-bind blocks chmod (EROFS) while still permitting connect() — verified
live: a real bwrap run shows chmod failing with "Read-only file system"
while a plain client still gets a reply over the same bind, and (for
contrast) the same run with --bind reproduces the original vulnerability
end to end (chmod succeeds, the host-side connect then fails with
EPERM). Added a live regression test proving both properties together.
…s editor

The panel's network type, options, and default fallback only knew
allow|deny. Since allowlist is now the shipped default, every user landed
on a dropdown showing no current selection and offering only Allow/Deny —
picking Allow silently replaced the default bounded policy with
unrestricted egress, with no way back through the GUI. Widens the type,
the option list (labelled to make bounded-vs-unrestricted explicit), and
every allowlist|deny fallback to match the backend/CLI contract, and adds
an "Extra allowed hosts" editor (mirrors the existing writable-paths
pattern) since the backend and CLI both already accept allowHosts.

Verified with a real render: a Vite SSR-load + happy-dom harness mounts
the panel through the app's actual context stack (PlatformProvider,
ServerProvider, GlobalSDKProvider) against a real in-process HTTP server
implementing the GET/PUT /settings/sandbox contract, confirming an
allowlist config renders as "Allowlist" (not blank) and that opening the
dropdown and picking Allow round-trips a real PATCH and re-renders the
new selection.
…rontend types

- ADR-0002 said macOS "has no namespace equivalent, so this enforcement
  argument does not transfer," implying the bounded-egress outcome itself
  is unreachable. Seatbelt reaches the same outcome via a different
  mechanism — (allow network-outbound (remote tcp "localhost:PORT")),
  which anthropic-experimental/sandbox-runtime ships — so it's achievable
  but unimplemented here, not impossible. Rewrote the paragraph
  accordingly.
- frontend/docs/.../sandbox.mdx never mentioned allowlist: claimed network
  is "allowed by default", documented only allow|deny for --network and
  the config key, and showed a "network": "deny" example. All contradicted
  the shipped allowlist default; updated the quick-start prose, the flag
  table (added --allow-host), and the config example/field list.
- frontend/workspace/src/notebook/runtime.ts labelled anything not
  === "deny" as "Network allowed", so an allowlist kernel read as fully
  open. kernelNetworkLabel/kernelNetworkTone now distinguish all three
  states (allowlist gets its own "Network bounded" label and a middle
  tone; unrestricted "allow" escalates to the danger tone). Also widened
  the stale KernelEnvironment.sandbox.network type to match the backend's
  three-state contract (science/kernel/types.ts).
- frontend/workspace/src/atlas/execution-authority.ts still typed
  sandbox.network as allow|deny, mismatched with the backend Decision type.
Seatbelt has no network namespace to sever the way bubblewrap's
--unshare-net does, so the host-side proxy listens on a loopback TCP
port instead of a unix socket, and seatbeltProfile narrows the
profile to exactly that port: (deny network*) always precedes a
single (allow network-outbound (remote ip "localhost:PORT")), and a
missing or invalid port throws rather than silently falling back to
a plain deny (which would read as network:"deny", not "allowlist")
or, worse, an unfiltered allow.

backend()/decide()/plan()/wrapArgv() and EgressRuntime.ensure() take
an injectable platform (default process.platform) since no Mac
exists on this project to run sandbox-exec on — the darwin branches
are only exercisable from Linux by overriding it. EgressRuntime
starts an Egress.serveShim bridge (TCP loopback -> the existing unix
socket) when the resolved backend is seatbelt, and egressFor returns
that bridged port, stringified, instead of the socket path.

No shim, launcher, or bundle is composed on darwin — the sandboxed
process dials the loopback proxy directly, so none of bubblewrap's
namespace-bridging machinery applies.
… the unix socket, and must require Proxy-Authorization

The prior commit on this branch (macOS seatbelt support) implemented
Task 7's egress path in a way that violates both design decisions the
brief marked as already made:

1. It added a host-side `Egress.serveShim` bridge (TCP loopback -> the
   existing unix socket) running in the CLI's own process for seatbelt,
   instead of having `serveProxy` listen on TCP directly. The brief is
   explicit that this extra hop must not exist.
2. It shipped no authentication at all on that loopback TCP port. A
   unix socket's access control is its filesystem permissions; a
   loopback port has none, so every process on the machine could reach
   the allowlist proxy. The brief requires a `Proxy-Authorization`
   secret, generated per proxy start, checked before anything else
   about a request (even whether it's malformed) is inspected, with a
   407 and no forwarding on a missing or wrong one.

This replaces the bridge with a real fix: `Egress.serveProxy` is now
overloaded to listen directly on either a unix socket or a
`hostname`/`port`, with a `secret` required (and enforced) only on the
TCP form — so each call site still gets back the concrete
`UnixSocketListener`/`TCPSocketListener` its own input implies.
`EgressRuntime` generates a `crypto.randomUUID()` secret once per
seatbelt proxy start and returns `"<port>:<secret>"` as the darwin
`egressFor()` value (bubblewrap keeps returning the unix socket path,
unaffected). `Sandbox.buildPolicy` splits that back into
`Policy.port`/`Policy.secret`, and `plan()`/`wrapArgv()` embed the
secret as userinfo in the proxy URL
(`http://os:<secret>@127.0.0.1:<port>`), which pip, curl and requests
all parse into a `Proxy-Authorization` header.

Test coverage: egress.test.ts gets direct unit tests against the TCP
listener (binds 127.0.0.1 only; a correctly-authenticated request
reaches the dial; a missing or wrong secret gets 407 and never reaches
the allowlist check or the dial; the unix-socket listener is
unaffected, no auth required there). egress-runtime.test.ts's darwin
tests are rewritten for the new shape (no more socket/bridge fields;
hostname+port+secret; the same both-directions auth assertions one
layer up, through the real lifecycle). sandbox.test.ts's darwin
plan()/wrapArgv() tests now use a `"port:secret"` egress value and
assert the authenticated proxy URL, plus a new case for a port with no
secret (must throw, not silently compose an unauthenticated URL).

Linux/bubblewrap paths are unchanged: bubblewrapArgs, serveShim (the
in-namespace bridge that already existed for bubblewrap), and the
unix-socket half of serveProxy are untouched logic, confirmed by diff
against this branch's pre-Task-7 tip and by the full live egress and
bwrap-shim suites passing unchanged (test/sandbox/: 97 pass, 0 fail;
full suite: 1944 pass / 1 skip / 1 pre-existing unrelated fail).
… fail closed on a cached-wrong-platform proxy, fix two tests, pin the auth seam with real clients

Task 7 review, four Important findings:

I3 (the one that mattered most): seatbeltProfile emitted only
network-outbound, spelled (remote ip ...) — narrower than, and a different
filter type than, the reference implementation
docs/adr/0002-sandbox-network-policy.md:56-59 already cites
(anthropic-experimental/sandbox-runtime: network-bind/network-inbound/
network-outbound, spelled tcp, all on the proxy's loopback port). An
independently-guessed narrower profile that has never been measured against
a real sandbox-exec is exactly how "allowlist" ships silently unreachable on
every Mac. Now emits all three operations, tcp-spelled, matching the ADR's
literal quote; the doc comment states plainly that whether network-bind/
network-inbound are even needed, and whether local/remote is the right
filter pairing for them, are still open questions only a Mac can answer.

I1: egressFor's seatbelt branch interpolated running.secret with no guard —
over a proxy already cached under a different injected platform, this
composed the literal string "3128:undefined" (truthy, so a bare
toBeTruthy() check on the secret half couldn't catch it). Now throws,
naming which listener is actually running; added a regression test that
forces the ordering and a stronger UUID-shaped assertion on the happy path.

I2: a test asserted the opposite of what its own comment claimed to prove,
passing for the wrong reason (127.0.0.1 isn't in DEFAULT_RULES, so the
request was denied at the allowlist check, never reaching the dial the test
claimed to exercise). Fixed by allowlisting 127.0.0.1 before starting the
proxy, so the request now genuinely clears auth and the allowlist check.

I4: every auth test hand-built the Proxy-Authorization header, leaving the
seam between proxyUrl()'s format and serveProxy's parser unpinned. Three
new tests drive real curl (absolute-form and --proxytunnel) and Python
urllib at the exact URL Sandbox.plan() composes.

Also: M1 (stop logging the secret half on an invalid egress warning), M5
(reject ports above 65535), M6 (update the ADR's now-stale "seatbelt falls
back to deny" line — the one docs/ line authorized for this round), M7
(the report's Mac-owner verification commands referenced an unassigned
shell variable and instructed running them after the proxy that backed them
had already been stopped; folded into one runnable script). M2/M3/M4/M8
left as instructed, with a note on each in the report.

Hit the same Bun.spawnSync-blocks-the-proxy's-own-event-loop deadlock this
codebase already has a comment about (sandbox.test.ts's "Bun.spawn, not
spawnSync") while writing the I4 tests; fixed by switching to async
Bun.spawn before it shipped.

test/sandbox/: 97 -> 104 pass, 0 fail. Full suite: 1944 -> 1951 pass / 1
skip / 1 fail, the fail pre-existing and unrelated.
… (fix round 2)

Fix round 2's only code change: writes the one item from that round meant
to be recorded in a doc comment rather than only in the Task 7 report — if
the host proxy dies while a seatbelt-sandboxed child is still alive,
network-bind/network-inbound on that same ephemeral port would let the
child itself bind or listen there. Confined to the one port the profile
names, not a broader grant; a real, specific consequence of matching the
ADR's reference shape, not a hypothetical one, so it belongs next to the
other open Mac-only questions already in this comment.

Round 2's other finding (M7 — the report's own verification script failed
on line 1 because Bun resolves a relative import against the importing
file's location, not cwd, and the report told a Mac owner to save the
script somewhere that broke that) is a report-only fix: corrected save
location, then run verbatim from a clean shell on this machine as far as
it allows. Both recorded in the report under "Fix round 2 of 5"
(.superpowers/, gitignored, not part of this commit).

test/sandbox/: 104 pass, 0 fail, unchanged by this round. Full suite: 1951
pass / 1 skip / 1 fail, the fail pre-existing and unrelated.
Windows has no sandbox backend today, so kernels are denied there
outright. Every network-filtering option for it needs administrator
rights, and asking for elevation to create a local account and load
kernel network filters — in order to run AI-authored code — is
indistinguishable at the UAC prompt from malware.

This inverts the model instead. An AppContainer without a network
capability has no network at all, kernel-enforced and unprivileged; a
named pipe ACL'd to its package SID gives it one channel to a broker
that performs approved requests on its behalf. No firewall mutation, no
elevation.

The cost is that Windows becomes capability-mediated rather than
socket-transparent: no network capability means no loopback either, so
the shim that lets unmodified pip and requests work on Linux cannot
exist. A notebook cell cannot fetch a scientific API directly. That is
recorded as a decision rather than discovered later.

Nothing here has been executed — there is no Windows machine on this
project. Four things a Windows owner must confirm first are listed, and
one of them would change the design if it came back the other way.
Task 7 built seatbelt support (profile text, authenticated loopback
proxy) entirely from Linux, with the platform injected on every
assertion, since no Mac exists on this project. Add the live test and
CI job that let a real sandbox-exec finally run it:

- test/sandbox/egress-live-seatbelt.test.ts: real sandbox-exec, real
  TCP-loopback Egress.serveProxy, real remote hosts, wired the way
  Sandbox.plan composes them in production — no platform override, so
  Sandbox.backend()/decide() resolve for real. Asserts an allowlisted
  host reaches 200 through the proxy, a denied host does not, direct
  egress with the proxy env unset fails, DNS resolves nothing inside
  the sandbox, and an 18MB wheel survives byte-for-byte. Gated on
  Sandbox.backend() === "seatbelt": skips on Linux, must fail rather
  than skip on the one machine that can run it.
- .github/workflows/ci.yml: new `sandbox` job, matrixed over
  ubuntu-latest/macos-latest (no windows-latest — Sandbox.backend()
  is "none" there), mirroring `migration`'s shape and reusing `test`'s
  bubblewrap install/apparmor workaround for the Linux leg.
The macOS CI leg found five failures, four of them in tests and one real.

Real: `shimScript`'s readiness cap was an iteration count (150 polls at
0.02s), which only equals the documented 3s where forking `sleep` is
nearly free. A macOS runner measured 17.1s for the same loop — ~114ms per
iteration, ~94ms of it fork/exec — a 5.7x overshoot. Any host with
expensive process creation drifts the same way. The loop now carries a
`date +%s` deadline alongside the count, probed exactly like fractional
`sleep` so a build without `%s` degrades to today's count-only behaviour
rather than skipping the wait. Measured with a fork-dominated `sleep`:
18.4s before, 3.3s after.

Tests: four assumed the ambient platform was bubblewrap, an assumption
written before the darwin branch existed and false on a macOS runner.
Three called `EgressRuntime.ensure()` and got a TCP listener where they
wanted a unix socket; the fourth composed bwrap argv through
`Sandbox.plan()` and hit `seatbeltProfile` instead. All four now inject
the platform through the seam that already exists for it. The over-broad
egress cases were passing on darwin for the wrong reason — they threw
"requires an egress port", not "requires an egress socket path" — so they
now assert the message too.

Also: prettier on docs/specs/windows-sandbox-design.md.
main moved four commits ahead while this branch was in review, and #277
("Match Claude Science compute, artifacts, and UI") rewrote the kernel,
notebook and pty files this branch also touches.

One real conflict, in `pty/index.ts`: main gave `terminalEnv` a fourth
`command` argument (it picks the PS1/PROMPT shape from the shell) and
computed the env before `Sandbox.wrapArgv`. This branch computes it after,
because `sandbox.env` carries the proxy variables the egress shim needs.
Kept this branch's ordering with main's new argument — reversing the order
would drop the proxy env on every terminal.

Everything else auto-merged. Verified rather than assumed: typecheck clean,
1953 backend tests pass, and the suites over the merged files specifically
(sandbox, server/notebook, pty-environment, frontend notebook runtime) are
green at 134 + 31.

One pre-existing local failure, untouched by this branch and passing in CI:
test/installation/native-package-matrix.test.ts indexes `npm pack --json`
output as an array, but npm 12 returns an object keyed by package name. It
will break CI too once the runner's npm bumps.
CodeQL flagged this as js/incomplete-url-substring-sanitization, high
severity. It is a false positive — `host` is the mounted DOM node and
`textContent` is rendered text, not a URL, and nothing here sanitizes
anything. The production matcher (`Egress.allowed`) splits the port off and
compares the host exactly or by suffix; it does no substring test.

The line was still wrong for a second reason worth fixing rather than
dismissing. It polled on the whole subtree's textContent containing the
host and then asserted on a <code> element's exact text — a looser wait
than the assertion, so the wait can finish while the assertion still fails,
burning all 50 iterations first. Both now use the same predicate.
The merge gate is that pip install works with the allowlist policy on every
platform we ship. Until now both live files stopped at curl, which proves
the boundary holds but not that it is usable: pip issues its own index
request, follows pypi.org -> files.pythonhosted.org (a second allowlist
entry, so this also covers a cross-host hop), streams a wheel and unpacks
it. None of that was exercised.

Both files run the same package with the same flags, deliberately, for the
same reason they already share the wheel URL and hash — a divergence
between backends should surface as one green and one red, not as two
different scenarios that both happen to pass.

`--only-binary :all:` keeps it a network test rather than a toolchain test.
The venv needs no network of its own: `python3 -m venv` bootstraps pip from
the interpreter's bundled ensurepip wheel, which is what makes this work on
a machine with no pip on PATH — one of the three original blockers.

The seatbelt test additionally covers pip authenticating to the proxy.
Seatbelt's loopback port is reachable by every process on the machine, so
the proxy URL carries a per-start secret and 407s anything without it; curl
and urllib were already covered, urllib3-on-CONNECT (what pip actually uses)
was not.

Linux: 3 pass, the pip test at 2.29s.
The spec and the (unwired) capability contract were written on
proto/kernel-package-install before the allowlist proxy existed. Both make
claims the proxy has since falsified, so they come across corrected rather
than verbatim.

The material one: "Redirect on failure" assumed a shell `pip install` fails
anyway, leaving the redirect's only job to replace a confusing error with a
helpful one. Under network "allowlist" it succeeds — measured in the agent's
own sandbox, no tool and no approval card involved:

  python3 -m venv <workspace>/venv && <workspace>/venv/bin/pip install tqdm  →  4.70.0

The workspace is writable and pypi is allowlisted, so read-only system
site-packages stops nothing; the agent builds its own venv beside the
project. The proxy did not create the intent to bypass, it removed the
accident that used to prevent it. So the shell path must be refused in the
bash tool before execution, not merely redirected after failure — otherwise
an agent that never calls the tool never shows a card, and the approval
gate is decorative. Recorded with its limits: refusal is a contract
boundary, not a security one, since the same egress can fetch a wheel by
hand.

`prompt.ts` said the same thing to the agent in its own words ("the agent
shell has no network"), which is now simply false. Rewritten to promise
refusal, and to name the venv-in-workspace route the old wording implied
was impossible.

Also refreshed "Not verified", which had gone stale in three entries: the
macOS proxy is now designed and verified against a real sandbox-exec, the
proxy's backpressure/bounds/timeouts are built and measured (concurrency
caps, audit log and hostile-upstream behaviour are still open), and the
release-mode shim is added as newly-known-untested.
Closes the hole the allowlist proxy opened. Before it, a shell `pip install`
died at DNS, so the install contract held by accident. Measured on
feat/sandbox-network-policy, this now succeeds with no tool and no approval
card:

  python3 -m venv <workspace>/venv && <workspace>/venv/bin/pip install tqdm

The workspace is writable and pypi is allowlisted, so read-only system
site-packages stops nothing. Until this lands, every part of the install
work that follows is decorative: an agent that never calls package_install
never shows a card.

Matching is over the tokenised argv bash.ts already builds from
tree-sitter, not the raw line — `echo "pip install numpy"` is one command
named `echo`, and a regex cannot tell the difference. Covers the routes a
bare `pip install` match misses: `<path>/bin/pip`, `python -m pip`,
`uv pip`, conda/mamba/poetry. Read-only subcommands (`list`, `show`,
`--version`) stay allowed; refusing them would break ordinary inspection.

The throw sits before any ctx.ask, so the user is never asked to approve a
command that is then refused anyway.

This is a contract boundary, not a security boundary — the same egress can
fetch a wheel by hand — and the code says so rather than claiming more.

Verified the wiring is load-bearing by removing it: two of the three
tool-boundary tests fail (the permission ask fires and the refusal message
never appears). 30 tests pass with it, typecheck clean, no regression in
the 133-test tool suite.
PackagePrompt was written during prototyping and never wired, so nothing
told the agent that package_install exists or that shell installers are
refused. Wired the way ComputePrompt already is — unconditionally, into the
system array on every request for every agent.

That unconditional injection is the load-bearing mechanism, not a skill
override. 199 of the 293 shipped SKILL.md files mention `pip install`, and
editing them would be neither necessary nor sufficient: the skill tool never
intercepts reference files, and skills cloned from GitHub are not this
repo's to edit. One block on every request reaches all of them.

Sequenced after the bash refusal deliberately — the contract now promises
something that is true.

29 package tests pass, 236 session tests unaffected, typecheck clean.
The manifest is the source of truth and the directory is derived, therefore
a cache — which is why they live in different roots. Global.Path.cache can
be cleared by the user or a cleaner at any time, and an environment has to
be rebuildable from its manifest afterwards; putting the manifest inside the
directory would turn a cache clean into unrecoverable data loss.

additive() is what decides whether kernels restart. Adding a package leaves
a live kernel correct because a new module imports on first use; an upgrade,
downgrade or removal does not, because a module already loaded stays at its
old version in memory while the files on disk disagree. That failure is
silent, which is why it is worse than an obvious restart — and why this is a
comparison rather than "restart on every install".

The lock chains on the previous entry with `previous.then(fn, fn)` so a
failed install does not cancel work queued behind it, and clears its slot in
a `finally` only when the slot is still its own. A lock surviving a throw
would brick that environment for the process lifetime — the same latching
bug the egress runtime shipped with, and the reason both cases are pinned by
tests.

16 tests, typecheck clean.
…edaction

A deliberate subset — name, extras, specifiers, markers, and the
`name @ url` form — with markers captured but never evaluated, because
nothing needs them. The spec's "real parser" requirement means specifically:
do not split on `==`, which mishandles `numpy>=2.4`, `pandas[performance]`
and `tqdm; python_version >= "3.9"`. Anything outside the grammar throws
rather than being guessed at, because a mis-parsed name becomes a wrong
permission pattern and a wrong pattern approves something other than what
runs.

The tests caught a real bug in the first implementation. Validating the
specifier with a prefix test, `/^(===|==|…|>|<)\s*\S/`, accepts `numpy >= `:
the alternation backtracks to the single-character `>` and consumes the `=`
as the version, so a dangling operator passes validation and reaches pip as
a literal requirement. Replaced with a clause regex anchored end to end and
applied per comma-separated clause, with the seven dangling-operator forms
pinned as regressions.

Names normalise per PEP 503 so Foo_Bar, Foo.Bar and foo-bar are one package
— treating them as three would let an upgrade look additive to
Environment.additive, which is what decides whether live kernels restart.

The pattern is names-only and sorted: sorted so the same set in a different
argument order matches an existing grant, names-only because resolution
happens after approval, so pinning a version must not fragment a grant the
user already gave. Index credentials are stripped before matching, so
rotating a token does not invalidate a standing grant and no secret reaches
a card.

39 tests, typecheck clean.
`npm pack --json` returns an array of entries on npm 11 and earlier, and an
object keyed by package name on npm 12. The test indexed [0], so it failed
with "npm pack did not return a tarball" on any machine running a current
npm while still passing on CI's older one — a green build hiding a broken
test, until the runner bumps and it goes red for everyone at once.

Accepts either shape rather than pinning a version: this test is about npm's
package selection across the native target matrix, not about its output
format.
The install runs in the same sandbox as the kernel, not a second more
permissive one — the allowlist proxy removed the asymmetry that justified a
separate install sandbox, so the only difference is that the environment
directory is writable.

Adding a real install test here rather than deferring it to the end-to-end
task immediately found a defect the rest of the suite could not see. The
ladder prefers uv when present, and `uv venv` does NOT bootstrap pip the way
`python3 -m venv` does, while install() shells out to `python -m pip`
regardless of who created the environment. So on any machine with uv the
ladder produced an environment the installer could not use: "No module named
pip", from a venv that looked perfectly healthy from outside the sandbox.
Every other test passed, because the one asserting a venv has pip forces the
venv branch explicitly.

Fixed with `uv venv --seed`. Seeding rather than adding a second
`uv pip install` path keeps one install code path to test and leaves the
environment usable by hand; the cost is a few hundred ms at creation only.
Pinned by a uv-branch test and an invariant test, so a future third branch
has to satisfy it too.

explain() translates the two failure surfaces that matter — the wheels-only
rejection that reads as "no such package", and a build failure whose summary
names the package while the `fatal error:` line above names the actually
missing system header. An unrecognised log passes through untouched;
inventing a diagnosis for an unanticipated failure is worse than showing it.

18 tests including a real tqdm install through bwrap with allowlist egress,
verified by reading the version back out of the environment rather than
trusting pip's exit code. Typecheck clean.
The ordinary permission contract, not modal's: installing a library must not
be gated more strictly than running arbitrary code, because it costs
nothing. So no digest, no spendFilter entry, and a readable canonical
command string as the pattern — `install tqdm → t1 [pypi.org/simple]` —
which changes whenever the approved action changes, so the prompt reappears
for free when it should. `always: ["install*"]` offers the standing grant
from the first card, mirroring notebook.ts.

Resolution happens after approval. Approving two names must not silently
approve the closure they pull in, so the card shows the request and freeze()
runs afterwards. A fully-satisfied request skips outright: no card, no
install, no restart, because nothing privileged happens.

Running the tool for real, rather than only reading its source, found a
silent data-loss bug. `execute` is reachable without zod having applied
parameter defaults; `language` was then undefined, JSON.stringify dropped
the key, and the manifest it wrote could never be parsed back. The
environment existed on disk with packages installed in it and was invisible
to the inventory — indistinguishable from "never created" at every call
site, with no error anywhere.

Fixed at the class rather than the instance: Environment.write now validates
before writing and throws naming the offending field, so no caller can
produce an unreadable manifest. The tool also defaults language explicitly.
TypeScript already enforces resolved params at the tool boundary — that is
belt and braces for other callers of write().

Both return branches now share one metadata shape; two shapes would force
every consumer to handle a union whose arms differ only in which keys exist.

restartEnvironment lands as a no-op with its final signature, so the tool has
no forward reference; the kernel-binding task gives it a body. Named
`boundEnvironment` rather than `environment` deliberately — the registry
entry already has an `environment` field of type KernelEnvironment, which is
the kernel's runtime context and nothing to do with packages.

114 package tests including three that run the real tool through a real
sandbox; 340 tool+science tests unaffected; typecheck clean.
…change

Binding is a property of the registry entry, never part of KernelIdentity —
that tuple is hashed into the storage key, so adding to it would orphan every
persisted record. It is named `boundEnvironment` because the entry already
has an `environment` field of type KernelEnvironment, which is the kernel's
runtime context (cwd, sandbox platform) and nothing to do with packages;
merging them would bind kernels to the wrong thing. Staleness is compared at
the registry level because ExecutionAuthority.require takes no kernel
identity and so cannot see which environment a kernel is bound to.

Writing a test that runs a real kernel, rather than asserting on plumbing,
found three defects:

1. The kernel could not see the environment at all — "No such file or
   directory" for an interpreter that exists. Production would have worked by
   luck, since ~/.cache is covered by `--ro-bind / /`, but `--tmpfs /tmp`
   masks it wherever the cache root lives under /tmp. Fixed with an explicit
   `readable` passthrough on wrapArgv. Deliberately read-only, not writable: a
   writable environment would let arbitrary kernel code run
   `subprocess.run([sys.executable, "-m", "pip", "install", ...])` over the
   same allowlisted egress, reopening through the notebook tool the exact
   bypass the bash-tool refusal closes.

2. wrapArgv replaced policy.readBind wholesale with the egress shim's paths at
   two call sites, silently discarding anything buildPolicy had put there.
   Merged instead. The env bind was being dropped on the floor with no error.

3. `six==1.17.0` against an installed 1.16.0 was reported "already installed".
   The skip check compared package NAMES only, so an upgrade became a silent
   no-op that also reported the change as additive — leaving the environment
   on the old version, telling the agent it had the new one, and leaving bound
   kernels un-restarted. Any requirement carrying a specifier, URL or extras
   now goes through pip, which already implements PEP 440 comparison and
   no-ops when the request is genuinely satisfied.

R binds by library path rather than interpreter, since it has no
per-environment binary: R_LIBS_USER, already in the kernel env allowlist,
also read-only so cell code cannot call install.packages() around the card.

restartEnvironment releases rather than respawns — kernels are lazy, so the
next cell boots a fresh one, and eager respawning would pay startup cost for
kernels the session may never touch again.

126 package tests, 446 sandbox+tool+science, typecheck clean. The behavioural
pair proves what plumbing tests cannot: a package installed into one
environment imports there and is genuinely absent in another real one, and an
additive install keeps kernel state while a version change discards it.
PackagePrompt.system() read a single global environments.json that nothing
has ever written, so the agent was told "No environments exist yet" forever
— including immediately after installing something. That makes the
contract's own first rule ("whether a package is available is a read-only
question, answer it from the inventory above") actively misleading: the
agent either installs what it already has or runs code to find out, both of
which the contract forbids.

Now assembled from the real per-project manifests. `busy` comes from the
live in-memory lock rather than a stored flag: a persisted flag would
survive a crash and permanently mark a healthy environment as installing,
with nothing to clear it.

The store import is aliased to `Store` because this namespace exports its
own `Environment` — the render schema — which shadows it inside every
function body here. Caught by typecheck, but it would have been a confusing
runtime failure.

Pinned by a test that installs for real and then reads the block back: it
says "No environments exist yet" before and lists "seen (python): tqdm"
after. 10 prompt tests, 236 session tests unaffected, typecheck clean.
`wait: true` stays the default and covers the common case — a two-second
install should cost one turn, not two. `wait: false` still takes the lock, so
a second install queues exactly as it would otherwise; what changes is that
the turn does not hold open. Its output deliberately carries no versions and
does not claim success, because there are none yet and inventing one is what
the contract forbids.

Reconcile is the half that matters. An install that cannot be proven still
running is `unknown`, never `fine`: pip has no transactions, so an
interrupted one may have left a partial tree, and silently trusting it turns
into a mystery ImportError several turns later.

Writing this against the real `science/kernel/process.ts` rather than the
plan's assumption corrected three things the plan had wrong. `token` was
module-private (now exported as `startToken`), synchronous rather than async,
and — the one that mattered — **undefined on Windows**, which has neither the
/proc nor the `ps -o lstart=` branch. The plan's rule, `running = Boolean(t)
&& t === stored`, would therefore have marked every Windows install unknown
forever and every environment permanently suspect. `matches()` already solves
this with `if (!identity.token) return true`; reconcile now shares that rule
through `KernelProcessIdentity.running(pid, token?)`, with the untokened case
pinned by its own test.

Claims live under Global.Path.state, not data: per-machine liveness should
not survive a restore onto another machine.

139 package tests, 340 tool+science unaffected, typecheck clean.
The simpler backend, as the spec predicted: no ladder to probe and no pip to
bootstrap, because install.packages is part of base R and the binding is a
library path rather than a per-environment interpreter. cran.r-project.org is
already in Egress.DEFAULT_RULES, so the allowlist is unchanged.

Only the backend differs by language. The card, the lock, the manifest write
and the additivity check are shared, because they are properties of the
contract rather than of pip or CRAN.

Two things R needs that Python does not:

- `install.packages()` signals failure with a warning and still exits 0, so
  the script checks installed.packages() afterwards and quits non-zero on
  anything missing. Without it a package that does not exist reads as a
  successful install.
- `lib` is passed explicitly as well as through R_LIBS_USER. Left to
  .libPaths() ordering, install.packages picks the first writable entry, which
  on a machine with a user library already configured is the wrong directory —
  and would leak the environment's packages into every other project.

Requirement.parse is deliberately NOT applied to R names. PEP 503
normalisation would turn data.table into data-table, which never matches what
CRAN installed; R names are case-sensitive and `.` is meaningful.

Verified where it can be: 146 package tests pass. The two live R tests SKIP on
this machine because Rscript is not installed, so the CRAN round trip itself
is unverified here — the same honest gap the macOS seatbelt work had before
CI could run it.
The condition for merging this work is that a package installs WITH THE
USER'S APPROVAL, under network "allowlist", on every platform we ship.
Everything else in test/package/ tests a component; this tests the claim.

Both halves are asserted together deliberately. A green install with an open
shell bypass is not the gate met — an agent that never calls the tool never
shows a card — so the refusal of `<venv>/bin/pip install`, `pip install`,
`uv pip install` and `python3 -m pip install` sits in the same file as the
approval assertion, not in an adjacent one.

The install assertion reads the version back out of the environment rather
than trusting pip's exit code, and checks that the policy in force really was
"allowlist" rather than a disabled sandbox — otherwise the test could pass
with no boundary at all.

The CI sandbox job now runs test/package/ alongside test/sandbox/ on both
legs, so the gate is a fact on Linux and macOS rather than a claim about one
of them. Timeout raised 20 -> 30 minutes: these are real installs against
real pypi, which the sandbox suite alone never did.

Locally: 255 pass / 5 skip / 0 fail for exactly what CI runs, and 2111 pass /
0 fail for the whole backend suite.
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// environment's packages into every other project on the machine.
expect(source.includes("R_LIBS_USER")).toBe(true)
expect(source.includes("install.packages")).toBe(true)
expect(source.includes("cran.r-project.org")).toBe(true)
test/package/ creates real projects with tmpdir({ git: true }), and
`git commit` exits 128 on a runner with no global user.name/user.email. The
`test` job has configured one for exactly this reason since before this
branch; the sandbox job never needed it until test/package/ joined it.

Ten failures on the first run of the new job, all of them this and none of
them the installs they looked like.
…ming it

The dead-pid reconcile test spawned /bin/true, awaited exit, and claimed the
pid — but `await proc.exited` is not the same as "the pid is gone". A
just-reaped child can stay signalable briefly, and on the macOS runner it
did: process.kill(pid, 0) still succeeded, so the claim reconciled as
"running" and the test failed for a reason that had nothing to do with
reconcile.

Now polls until the premise actually holds and asserts it, so a future
failure here means reconcile is wrong rather than that the fixture raced.
/bin/true does not exist on macOS — it is /usr/bin/true — so posix_spawn
returned ENOENT and the dead-pid reconcile test failed there for a reason
unrelated to reconcile. My first reading of that red run blamed a zombie pid
still being signalable; the polling added for it is reasonable hardening and
stays, but it was not the cause.

Uses process.execPath, which is present by definition.
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