fix: complete P2 host workspace contract

docs/contracts/workspace-preprocessing-cli.md

@@ -1,19 +1,21 @@
 # Workspace preprocessing CLI contract
 
-`thothctl workspace` is a closed native host interface. It accepts only the commands and options listed below; unknown options, passthrough separators, shell fragments, and bootstrap run selectors are rejected before Compose is invoked.
+`thothctl workspace` is a closed native host interface. Only the seven paths below are representable; there is no passthrough, shell, arbitrary child argv, or host-selected bootstrap run ID.
 
 ```text
-thothctl --installation /absolute/thothii-installation.yaml workspace inspect --workspace ID [--json]
-thothctl ... workspace preprocess dwh --workspace ID [--resume RUN] [--json]
-thothctl ... workspace schema suggest-fks --workspace ID [--from-sql FILE]... [--assume COLUMN=TABLE]... [--output FILE] [--json]
-thothctl ... workspace schema check --workspace ID --resume RUN [--annotations FILE --reviewed-candidates sha256:HEX] [--json]
-thothctl ... workspace index-schema --workspace ID [--json]
-thothctl ... workspace preprocess evidence --workspace ID [--dry-run] [--resume RUN] [--json]
-thothctl ... workspace preprocess run --workspace ID [--resume RUN] [--json]
+workspace inspect --workspace ID [--json]
+workspace preprocess dwh --workspace ID [--resume RUN] [--json]
+workspace schema suggest-fks --workspace ID [--from-sql FILE]... [--assume COLUMN=TABLE]... [--output FILE] [--json]
+workspace schema check --workspace ID --resume RUN [--annotations FILE --reviewed-candidates sha256:HEX] [--json]
+workspace index-schema --workspace ID [--json]
+workspace preprocess evidence --workspace ID [--dry-run] [--resume RUN] [--json]
+workspace preprocess run --workspace ID [--resume RUN] [--json]
 ```
 
-Workspace IDs are lowercase `[a-z][a-z0-9-]{2,62}` and outer run IDs are exactly 32 lowercase hexadecimal characters. SQL ingress is limited to 32 regular, canonical, non-symlink files of at most 1 MiB each and 16 MiB total. Annotation ingress is UTF-8 and at most 16 MiB. Inputs are read without following links and are never mounted as host directories. Suggestion candidate output is bounded to 700 KiB.
+IDs are lowercase `[a-z][a-z0-9-]{2,62}` and outer run IDs are exactly 32 lowercase hexadecimal characters. `--from-sql` accepts at most 32 canonical regular non-symlink files, each at most 1 MiB and 16 MiB total. `--assume` accepts at most 256 values of 256 bytes, each matching `column=table`. Annotations are one canonical UTF-8 file at most 16 MiB. Existing output, links, hardlinks, directories, replacement races, and reparse points are refused with a generic unsafe-file error.
 
-`workspace inspect` has no resume or bootstrap option. Bootstrap recovery is automatic and installation-scoped; the host never chooses a run ID. `schema check` requires an explicit outer run ID and requires `--annotations` and `--reviewed-candidates` together.
+The bounded schema-v1 stdin request contains only operation-appropriate fields. SQL and annotations are represented by a logical basename, base64 bytes, and a declared `sha256:<hex>` digest; no host path or raw content enters the request. The complete request is at most 1 MiB, has exactly one JSON value, and cannot replace command-derived fields. Candidate responses may carry the internal `hostExport` (`mediaType`, `sha256`, `contentBase64`) only for `suggest-fks`; it is verified (UTF-8 YAML, digest, and 700 KiB maximum), removed from the public result, and written exclusively only after result/run/identity validation.
 
-The one-shot operation emits one schema-v1 JSON envelope. Stdout is capped at 1 MiB and sanitized stderr at 64 KiB. Exit status is 0 for success/unchanged/dry-run, 3 for an expected blocked/manual checkpoint, 2 for command or unsafe-file errors, and 1 for operational failures.
+The public result has schema version 1 and only these fields: `status`, `code`, workspace/revision/descriptor/operation identities, optional run and child run IDs, completed stages, counts, artifact identities, and warnings. Revisions/descriptors are 40-hex; run IDs are 32-hex; artifact digests are `sha256:<hex>`. A nonzero child exit is accepted only for the matching blocked (3) or failed (1) result. Stdout is capped at 1 MiB and stderr at 64 KiB. Compose is invoked only as `compose run --rm --no-deps --no-TTY workspace-maintenance ...`; output never includes child stderr or secrets.
+
+Exit 0 means succeeded, unchanged, or dry-run; exit 3 means an expected operator checkpoint/block; exit 2 means grammar or unsafe local-file failure; exit 1 means operational failure. Human mode prints only allowlisted identity/status fields. For `registry_bootstrap_recovery_conflict` it prints exactly: `Bootstrap recovery is ambiguous or corrupt; inspect the installation registry jobs.`

tools/thothctl/cmd/thothctl/main.go

@@ -90,11 +90,48 @@ func run(ctx context.Context, args []string, stdout, stderr io.Writer) int {
 	runner := compose.NewRunner("")
 	if command == "workspace" {
 		workspaceCommand, parseErr := workspaceops.ParseWorkspaceCommand(append([]string{"workspace"}, commandArgs...))
-		if parseErr != nil { return commandUsageError(stderr, parseErr.Error()) }
+		if parseErr != nil {
+			return commandUsageError(stderr, parseErr.Error())
+		}
 		result, operationErr := workspaceops.Run(ctx, installation, runner, workspaceCommand, nil)
-		if operationErr != nil { if errors.Is(operationErr, compose.ErrOutputLimit) || strings.Contains(operationErr.Error(), "unsafe") || strings.Contains(operationErr.Error(), "exceeds") { return commandUsageError(stderr, operationErr.Error()) }; fmt.Fprintf(stderr, "thothctl: %s\n", output.Sanitize(operationErr.Error(), secretValues)); return 1 }
-		if err := json.NewEncoder(stdout).Encode(result); err != nil { return 1 }
-		if result.Status == "blocked" { return 3 }; if result.Status == "failed" { return 1 }; return 0
+		if operationErr != nil {
+			if errors.Is(operationErr, compose.ErrOutputLimit) || strings.Contains(operationErr.Error(), "unsafe") || strings.Contains(operationErr.Error(), "exceeds") || strings.Contains(operationErr.Error(), "invalid workspace") {
+				return commandUsageError(stderr, operationErr.Error())
+			}
+			fmt.Fprintf(stderr, "thothctl: %s\n", output.Sanitize(operationErr.Error(), secretValues))
+			return 1
+		}
+		jsonMode := true
+		switch c := workspaceCommand.(type) {
+		case workspaceops.InspectCommand:
+			jsonMode = c.JSON
+		case workspaceops.DwhRequest:
+			jsonMode = c.JSON
+		case workspaceops.SuggestFksRequest:
+			jsonMode = c.JSON
+		case workspaceops.CheckSchemaRequest:
+			jsonMode = c.JSON
+		case workspaceops.IndexSchemaRequest:
+			jsonMode = c.JSON
+		case workspaceops.EvidenceRequest:
+			jsonMode = c.JSON
+		case workspaceops.RunRequest:
+			jsonMode = c.JSON
+		}
+		if jsonMode {
+			if err := json.NewEncoder(stdout).Encode(result); err != nil {
+				return 1
+			}
+		} else {
+			renderWorkspaceHuman(stdout, result)
+		}
+		if result.Status == "blocked" {
+			return 3
+		}
+		if result.Status == "failed" {
+			return 1
+		}
+		return 0
 	}
 	var result compose.Result
 	switch command {
@@ -173,6 +210,20 @@ func run(ctx context.Context, args []string, stdout, stderr io.Writer) int {
 	return writeResult(result, err, secretValues, stdout, stderr)
 }
 
+func renderWorkspaceHuman(w io.Writer, result workspaceops.Result) {
+	if result.Code == workspaceops.CodeRegistryBootstrapRecoveryConflict {
+		fmt.Fprintln(w, "Bootstrap recovery is ambiguous or corrupt; inspect the installation registry jobs.")
+		return
+	}
+	fmt.Fprintf(w, "Workspace %s: %s (%s)\n", result.WorkspaceID, result.Status, result.Code)
+	if result.RunID != "" {
+		fmt.Fprintf(w, "Run: %s\n", result.RunID)
+	}
+	if len(result.CompletedStages) > 0 {
+		fmt.Fprintf(w, "Completed stages: %s\n", strings.Join(result.CompletedStages, ", "))
+	}
+}
+
 func writeRemovalTargets(outputWriter io.Writer, project string, targets []serverops.Container) {
 	fmt.Fprintf(outputWriter, "Removal targets for installation project %s:\n", project)
 	if len(targets) == 0 {

tools/thothctl/cmd/thothctl/main_test.go

@@ -15,6 +15,7 @@ import (
 	"github.com/aritmolab/thothii/tools/thothctl/internal/config"
 	"github.com/aritmolab/thothii/tools/thothctl/internal/pi"
 	"github.com/aritmolab/thothii/tools/thothctl/internal/testsupport"
+	"github.com/aritmolab/thothii/tools/thothctl/internal/workspaceops"
 )
 
 func TestInstallationRunnerMapsProfileToSessionInventoryScope(t *testing.T) {
@@ -846,3 +847,11 @@ func assertInvocationContains(t *testing.T, invocations [][]string, want ...stri
 	}
 	t.Fatalf("invocations = %#v, want %#v", invocations, want)
 }
+
+func TestRenderWorkspaceHumanHidesRecoveryIdentity(t *testing.T) {
+	var out bytes.Buffer
+	renderWorkspaceHuman(&out, workspaceops.Result{WorkspaceID: "psd", Status: "blocked", Code: workspaceops.CodeRegistryBootstrapRecoveryConflict, RunID: "0123456789abcdef0123456789abcdef"})
+	if out.String() != "Bootstrap recovery is ambiguous or corrupt; inspect the installation registry jobs.\n" {
+		t.Fatalf("human output = %q", out.String())
+	}
+}

tools/thothctl/internal/compose/process_unix.go

@@ -1,5 +1,18 @@
 //go:build !windows
+
 package compose
-import ("os/exec"; "syscall")
-func configureOwnedProcess(c *exec.Cmd) { c.SysProcAttr=&syscall.SysProcAttr{Setpgid:true} }
-func terminateOwnedProcess(c *exec.Cmd) { if c.Process!=nil { _=syscall.Kill(-c.Process.Pid, syscall.SIGKILL); _=c.Process.Kill() } }
+
+import (
+	"os/exec"
+	"syscall"
+)
+
+func configureOwnedProcess(c *exec.Cmd)      { c.SysProcAttr = &syscall.SysProcAttr{Setpgid: true} }
+func registerOwnedProcess(c *exec.Cmd) error { return nil }
+func releaseOwnedProcess(c *exec.Cmd)        {}
+func terminateOwnedProcess(c *exec.Cmd) {
+	if c.Process != nil {
+		_ = syscall.Kill(-c.Process.Pid, syscall.SIGKILL)
+		_ = c.Process.Kill()
+	}
+}

tools/thothctl/internal/compose/process_windows.go

@@ -1,5 +1,51 @@
 //go:build windows
+
 package compose
-import ("os/exec"; "syscall")
-func configureOwnedProcess(c *exec.Cmd) { c.SysProcAttr=&syscall.SysProcAttr{} }
-func terminateOwnedProcess(c *exec.Cmd) { if c.Process!=nil { _=c.Process.Kill() } }
+
+import (
+	"golang.org/x/sys/windows"
+	"os/exec"
+	"sync"
+)
+
+var ownedJobs = struct {
+	sync.Mutex
+	m map[*exec.Cmd]windows.Handle
+}{m: make(map[*exec.Cmd]windows.Handle)}
+
+func configureOwnedProcess(c *exec.Cmd) {
+	c.SysProcAttr = &windows.SysProcAttr{CreationFlags: windows.CREATE_NEW_PROCESS_GROUP}
+}
+func registerOwnedProcess(c *exec.Cmd) error {
+	h, err := windows.CreateJobObject(nil, nil)
+	if err != nil {
+		return err
+	}
+	if err = windows.AssignProcessToJobObject(h, windows.Handle(c.Process.Pid)); err != nil {
+		windows.CloseHandle(h)
+		return err
+	}
+	ownedJobs.Lock()
+	ownedJobs.m[c] = h
+	ownedJobs.Unlock()
+	return nil
+}
+func releaseOwnedProcess(c *exec.Cmd) {
+	ownedJobs.Lock()
+	h := ownedJobs.m[c]
+	delete(ownedJobs.m, c)
+	ownedJobs.Unlock()
+	if h != 0 {
+		windows.CloseHandle(h)
+	}
+}
+func terminateOwnedProcess(c *exec.Cmd) {
+	ownedJobs.Lock()
+	h := ownedJobs.m[c]
+	ownedJobs.Unlock()
+	if h != 0 {
+		_ = windows.TerminateJobObject(h, 1)
+	} else if c.Process != nil {
+		_ = c.Process.Kill()
+	}
+}

tools/thothctl/internal/compose/runner.go

@@ -7,111 +7,154 @@ import (
 	"errors"
 	"fmt"
 	"io"
-	"sync"
 	"os"
 	"os/exec"
+	"sync"
 )
 
-// Result is the captured output and process exit code for one Docker invocation.
 var ErrOutputLimit = errors.New("compose output limit exceeded")
 
-// CaptureLimits bounds each stream independently. Overflow is never retained.
-type CaptureLimits struct { StdoutBytes int64; StderrBytes int64 }
-
+type CaptureLimits struct {
+	StdoutBytes int64
+	StderrBytes int64
+}
 type Result struct {
 	Stdout   string
 	Stderr   string
 	ExitCode int
 }
+type Runner struct{ binary string }
 
-// Runner executes the Docker CLI. It never invokes a shell.
-type Runner struct {
-	binary string
-}
-
-// NewRunner returns a runner for binary. An empty binary selects docker from PATH.
 func NewRunner(binary string) Runner {
 	if binary == "" {
 		binary = "docker"
 	}
 	return Runner{binary: binary}
 }
-
-// Run invokes Docker with the supplied argument array and optional standard input.
 func (r Runner) Run(ctx context.Context, args []string, stdin io.Reader) (Result, error) {
-	command := exec.CommandContext(ctx, r.binary, args...)
-	command.Stdin = stdin
-	var stdout, stderr bytes.Buffer
-	command.Stdout = &stdout
-	command.Stderr = &stderr
-	err := command.Run()
-	result := Result{Stdout: stdout.String(), Stderr: stderr.String()}
+	c := exec.CommandContext(ctx, r.binary, args...)
+	c.Stdin = stdin
+	var out, er bytes.Buffer
+	c.Stdout = &out
+	c.Stderr = &er
+	err := c.Run()
+	res := Result{Stdout: out.String(), Stderr: er.String()}
 	if err == nil {
-		return result, nil
+		return res, nil
 	}
-	var exitError *exec.ExitError
-	if errors.As(err, &exitError) {
-		result.ExitCode = exitError.ExitCode()
-		return result, err
+	var x *exec.ExitError
+	if errors.As(err, &x) {
+		res.ExitCode = x.ExitCode()
+		return res, err
 	}
 	if errors.Is(err, exec.ErrNotFound) || errors.Is(err, os.ErrNotExist) {
-		result.ExitCode = 127
-		return result, fmt.Errorf("%w: %w", exec.ErrNotFound, err)
+		res.ExitCode = 127
+		return res, fmt.Errorf("%w: %w", exec.ErrNotFound, err)
 	}
-	return result, err
+	return res, err
 }
 
-
-// RunBounded executes one owned process while retaining at most the configured bytes per stream.
-// The complete process group is terminated as soon as either stream exceeds its limit.
+// RunBounded streams each pipe into a preallocated fixed-capacity collector. It owns the
+// process group and tears it down on the first overflow or cancellation.
 func (r Runner) RunBounded(ctx context.Context, args []string, stdin io.Reader, limits CaptureLimits) (Result, error) {
-	if limits.StdoutBytes < 0 || limits.StderrBytes < 0 { return Result{}, ErrOutputLimit }
-	command := exec.Command(r.binary, args...)
-	command.Stdin = stdin
-	stdoutPipe, err := command.StdoutPipe(); if err != nil { return Result{}, err }
-	stderrPipe, err := command.StderrPipe(); if err != nil { return Result{}, err }
-	configureOwnedProcess(command)
-	if err := command.Start(); err != nil { return Result{ExitCode: 127}, err }
-	type stream struct { b []byte; overflow bool }
-	var out, er stream
+	if limits.StdoutBytes < 0 || limits.StderrBytes < 0 {
+		return Result{}, ErrOutputLimit
+	}
+	c := exec.Command(r.binary, args...)
+	c.Stdin = stdin
+	op, err := c.StdoutPipe()
+	if err != nil {
+		return Result{}, err
+	}
+	ep, err := c.StderrPipe()
+	if err != nil {
+		return Result{}, err
+	}
+	configureOwnedProcess(c)
+	if err = c.Start(); err != nil {
+		return Result{ExitCode: 127}, err
+	}
+	if err = registerOwnedProcess(c); err != nil {
+		terminateOwnedProcess(c)
+		_ = c.Wait()
+		return Result{}, err
+	}
+	defer releaseOwnedProcess(c)
+	type collector struct {
+		buf      []byte
+		n        int64
+		overflow bool
+	}
+	out := collector{buf: make([]byte, limits.StdoutBytes)}
+	er := collector{buf: make([]byte, limits.StderrBytes)}
 	overflow := make(chan struct{}, 1)
-	var wg sync.WaitGroup; wg.Add(2)
-	read := func(rd io.Reader, max int64, target *stream) {
+	var wg sync.WaitGroup
+	wg.Add(2)
+	read := func(rd io.Reader, max int64, col *collector) {
 		defer wg.Done()
-		buf := make([]byte, 32*1024)
+		chunk := make([]byte, 32*1024)
 		for {
-			n, readErr := rd.Read(buf)
+			n, e := rd.Read(chunk)
 			if n > 0 {
-				remain := max - int64(len(target.b))
-				if remain > 0 { take := int64(n); if take > remain { take = remain }; target.b = append(target.b, buf[:take]...) }
+				remain := max - col.n
+				if remain > 0 {
+					take := int64(n)
+					if take > remain {
+						take = remain
+					}
+					copy(col.buf[col.n:col.n+take], chunk[:take])
+					col.n += take
+				}
 				if int64(n) > remain {
-					target.overflow = true
-					select { case overflow <- struct{}{}: default: }
+					col.overflow = true
+					select {
+					case overflow <- struct{}{}:
+					default:
+					}
 					return
 				}
 			}
-			if readErr != nil { return }
+			if e != nil {
+				return
+			}
 		}
 	}
-	go read(stdoutPipe, limits.StdoutBytes, &out); go read(stderrPipe, limits.StderrBytes, &er)
-	finished := make(chan error, 1); go func() { finished <- command.Wait() }()
+	go read(op, limits.StdoutBytes, &out)
+	go read(ep, limits.StderrBytes, &er)
+	waited := make(chan error, 1)
+	go func() { waited <- c.Wait() }()
 	var waitErr error
+	var cancelled error
 	select {
-	case waitErr = <-finished:
-		// The parent may exit while a descendant inherited stdout/stderr; tear down the owned group.
-		terminateOwnedProcess(command)
+	case waitErr = <-waited:
+		terminateOwnedProcess(c)
 	case <-overflow:
-		terminateOwnedProcess(command); waitErr = <-finished
+		terminateOwnedProcess(c)
+		waitErr = <-waited
 	case <-ctx.Done():
-		terminateOwnedProcess(command); waitErr = <-finished
+		cancelled = ctx.Err()
+		terminateOwnedProcess(c)
+		waitErr = <-waited
 	}
 	wg.Wait()
-	result := Result{Stdout: string(out.b), Stderr: string(er.b)}
-	if out.overflow || er.overflow { return result, ErrOutputLimit }
-	if waitErr == nil { return result, nil }
-	var exitErr *exec.ExitError
-	if errors.As(waitErr, &exitErr) { result.ExitCode = exitErr.ExitCode(); return result, waitErr }
-	if errors.Is(waitErr, exec.ErrNotFound) || errors.Is(waitErr, os.ErrNotExist) { result.ExitCode = 127; return result, fmt.Errorf("%w: %w", exec.ErrNotFound, waitErr) }
-	if ctx.Err() != nil { return result, ctx.Err() }
-	return result, waitErr
+	res := Result{Stdout: string(out.buf[:out.n]), Stderr: string(er.buf[:er.n])}
+	if out.overflow || er.overflow {
+		return res, ErrOutputLimit
+	}
+	if cancelled != nil {
+		return res, cancelled
+	}
+	if waitErr == nil {
+		return res, nil
+	}
+	var ex *exec.ExitError
+	if errors.As(waitErr, &ex) {
+		res.ExitCode = ex.ExitCode()
+		return res, waitErr
+	}
+	if errors.Is(waitErr, exec.ErrNotFound) || errors.Is(waitErr, os.ErrNotExist) {
+		res.ExitCode = 127
+		return res, fmt.Errorf("%w: %w", exec.ErrNotFound, waitErr)
+	}
+	return res, waitErr
 }

tools/thothctl/internal/compose/runner_test.go

@@ -6,8 +6,10 @@ import (
 	"os"
 	"os/exec"
 	"path/filepath"
+	"runtime"
 	"strings"
 	"testing"
+	"time"
 )
 
 func TestRunnerPassesEachArgumentWithoutShellSplitting(t *testing.T) {
@@ -65,18 +67,78 @@ func writeExecutable(t *testing.T, contents string) string {
 	return path
 }
 
-
 func TestRunnerBoundedCapturesExactlyAtLimit(t *testing.T) {
 	runner := NewRunner(writeExecutable(t, "#!/bin/sh\nprintf 1234567890\nprintf error12345 >&2\n"))
 	result, err := runner.RunBounded(context.Background(), nil, nil, CaptureLimits{StdoutBytes: 10, StderrBytes: 10})
-	if err != nil { t.Fatal(err) }
-	if result.Stdout != "1234567890" || result.Stderr != "error12345" { t.Fatalf("bounded result = %#v", result) }
+	if err != nil {
+		t.Fatal(err)
+	}
+	if result.Stdout != "1234567890" || result.Stderr != "error12345" {
+		t.Fatalf("bounded result = %#v", result)
+	}
 }
 
 func TestRunnerBoundedRejectsOneByteOverEachStream(t *testing.T) {
 	for _, script := range []string{"#!/bin/sh\nprintf 12345678901\n", "#!/bin/sh\nprintf 12345678901 >&2\n"} {
-		runner := NewRunner(writeExecutable(t, script)); result, err := runner.RunBounded(context.Background(), nil, nil, CaptureLimits{StdoutBytes: 10, StderrBytes: 10})
-		if !errors.Is(err, ErrOutputLimit) { t.Fatalf("err = %v result=%#v", err, result) }
-		if len(result.Stdout) > 10 || len(result.Stderr) > 10 { t.Fatalf("retained overflow: %#v", result) }
+		runner := NewRunner(writeExecutable(t, script))
+		result, err := runner.RunBounded(context.Background(), nil, nil, CaptureLimits{StdoutBytes: 10, StderrBytes: 10})
+		if !errors.Is(err, ErrOutputLimit) {
+			t.Fatalf("err = %v result=%#v", err, result)
+		}
+		if len(result.Stdout) > 10 || len(result.Stderr) > 10 {
+			t.Fatalf("retained overflow: %#v", result)
+		}
+	}
+}
+
+func TestRunnerBoundedTerminatesInfiniteStreams(t *testing.T) {
+	for _, script := range []string{"#!/bin/sh\nwhile :; do printf x; done", "#!/bin/sh\nwhile :; do printf x >&2; done"} {
+		runner := NewRunner(writeExecutable(t, script))
+		result, err := runner.RunBounded(context.Background(), nil, nil, CaptureLimits{StdoutBytes: 1024, StderrBytes: 1024})
+		if !errors.Is(err, ErrOutputLimit) {
+			t.Fatalf("err = %v result = %#v", err, result)
+		}
+		if len(result.Stdout) > 1024 || len(result.Stderr) > 1024 {
+			t.Fatalf("retained overflow: %#v", result)
+		}
+	}
+}
+
+func TestRunnerBoundedCancellationWinsOverChildKill(t *testing.T) {
+	ctx, cancel := context.WithCancel(context.Background())
+	runner := NewRunner(writeExecutable(t, "#!/bin/sh\nsleep 30\n"))
+	done := make(chan error, 1)
+	go func() {
+		_, err := runner.RunBounded(ctx, nil, nil, CaptureLimits{StdoutBytes: 32, StderrBytes: 32})
+		done <- err
+	}()
+	cancel()
+	select {
+	case err := <-done:
+		if !errors.Is(err, context.Canceled) {
+			t.Fatalf("err = %v", err)
+		}
+	case <-time.After(3 * time.Second):
+		t.Fatal("cancellation did not terminate process")
+	}
+}
+
+func TestRunnerBoundedTerminatesGrandchildHoldingPipe(t *testing.T) {
+	if runtime.GOOS == "windows" {
+		t.Skip("shell process-group fixture is Unix-specific")
+	}
+	runner := NewRunner(writeExecutable(t, "#!/bin/sh\n(sleep 30; printf survivor) &\nwhile :; do printf x; done\n"))
+	done := make(chan error, 1)
+	go func() {
+		_, err := runner.RunBounded(context.Background(), nil, nil, CaptureLimits{StdoutBytes: 64, StderrBytes: 64})
+		done <- err
+	}()
+	select {
+	case err := <-done:
+		if !errors.Is(err, ErrOutputLimit) {
+			t.Fatalf("err = %v", err)
+		}
+	case <-time.After(3 * time.Second):
+		t.Fatal("grandchild kept owned pipe alive")
 	}
 }

tools/thothctl/internal/config/installation_test.go

@@ -178,7 +178,11 @@ func TestLoadRejectsRelativeInstallationPaths(t *testing.T) {
 func writeInstallation(t *testing.T, profile string) (string, string, string, string) {
 	t.Helper()
 
-	root := filepath.Join(t.TempDir(), "installation folder with spaces")
+	rootBase, err := filepath.EvalSymlinks(t.TempDir())
+	if err != nil {
+		t.Fatal(err)
+	}
+	root := filepath.Join(rootBase, "installation folder with spaces")
 	projectDirectory := filepath.Join(root, "project directory with spaces")
 	if err := os.MkdirAll(filepath.Join(projectDirectory, "deploy"), 0o755); err != nil {
 		t.Fatal(err)

tools/thothctl/internal/safeio/files_unix.go

@@ -56,9 +56,19 @@ func ReadCanonicalRegular(path string, maximum int64) ([]byte, error) {
 	if err != nil {
 		return nil, ErrUnsafeFile
 	}
+	// Checking the retained descriptor alone misses a pathname replacement while the
+	// read is in progress.  The parent descriptor and final name must still resolve to
+	// the exact open file after reading.
 	if err := unix.Fstat(int(file.Fd()), &after); err != nil || after.Nlink > 1 || after.Mode != before.Mode || after.Ino != before.Ino || after.Dev != before.Dev || after.Size != before.Size {
 		return nil, ErrUnsafeFile
 	}
+	var named unix.Stat_t
+	if err := unix.Fstatat(directory, components[len(components)-1], &named, unix.AT_SYMLINK_NOFOLLOW); err != nil || named.Nlink > 1 || named.Mode != before.Mode || named.Ino != before.Ino || named.Dev != before.Dev {
+		return nil, ErrUnsafeFile
+	}
+	if !recheckUnixParents(components, directories) {
+		return nil, ErrUnsafeFile
+	}
 	return contents, nil
 }
 
@@ -89,6 +99,10 @@ func writeCanonicalExclusive(path string, contents []byte, mode fs.FileMode) err
 		unix.Close(dir)
 		dir = next
 	}
+	var parentBefore unix.Stat_t
+	if err := unix.Fstat(dir, &parentBefore); err != nil {
+		return ErrUnsafeFile
+	}
 	fd, err := unix.Openat(dir, components[len(components)-1], unix.O_WRONLY|unix.O_CREAT|unix.O_EXCL|unix.O_CLOEXEC|unix.O_NOFOLLOW, uint32(mode.Perm()))
 	if err != nil {
 		return ErrUnsafeFile
@@ -108,6 +122,16 @@ func writeCanonicalExclusive(path string, contents []byte, mode fs.FileMode) err
 	if err := f.Sync(); err != nil {
 		return ErrUnsafeFile
 	}
+	var opened, named, parentAfter unix.Stat_t
+	if err := unix.Fstat(fd, &opened); err != nil || opened.Nlink != 1 {
+		return ErrUnsafeFile
+	}
+	if err := unix.Fstatat(dir, components[len(components)-1], &named, unix.AT_SYMLINK_NOFOLLOW); err != nil || named.Nlink != 1 || named.Ino != opened.Ino || named.Dev != opened.Dev {
+		return ErrUnsafeFile
+	}
+	if err := unix.Fstat(dir, &parentAfter); err != nil || parentAfter.Ino != parentBefore.Ino || parentAfter.Dev != parentBefore.Dev || !recheckUnixParentPath(components[:len(components)-1], dir) {
+		return ErrUnsafeFile
+	}
 	return nil
 }
 
@@ -140,3 +164,46 @@ func validateCanonicalOutputPath(path string) error {
 	}
 	return nil
 }
+
+func recheckUnixParents(components []string, retained []int) bool {
+	if len(retained) != len(components) {
+		return false
+	}
+	dir, err := unix.Open("/", unix.O_RDONLY|unix.O_DIRECTORY|unix.O_CLOEXEC, 0)
+	if err != nil {
+		return false
+	}
+	defer unix.Close(dir)
+	for i, component := range components[:len(components)-1] {
+		next, e := unix.Openat(dir, component, unix.O_RDONLY|unix.O_DIRECTORY|unix.O_CLOEXEC|unix.O_NOFOLLOW, 0)
+		if e != nil {
+			return false
+		}
+		var got, want unix.Stat_t
+		if unix.Fstat(next, &got) != nil || unix.Fstat(retained[i+1], &want) != nil || got.Ino != want.Ino || got.Dev != want.Dev {
+			unix.Close(next)
+			return false
+		}
+		unix.Close(dir)
+		dir = next
+	}
+	return true
+}
+
+func recheckUnixParentPath(components []string, retained int) bool {
+	dir, err := unix.Open("/", unix.O_RDONLY|unix.O_DIRECTORY|unix.O_CLOEXEC, 0)
+	if err != nil {
+		return false
+	}
+	defer unix.Close(dir)
+	for _, component := range components {
+		next, e := unix.Openat(dir, component, unix.O_RDONLY|unix.O_DIRECTORY|unix.O_CLOEXEC|unix.O_NOFOLLOW, 0)
+		if e != nil {
+			return false
+		}
+		unix.Close(dir)
+		dir = next
+	}
+	var got, want unix.Stat_t
+	return unix.Fstat(dir, &got) == nil && unix.Fstat(retained, &want) == nil && got.Ino == want.Ino && got.Dev == want.Dev
+}

tools/thothctl/internal/safeio/files_windows.go

@@ -54,7 +54,29 @@ func ReadCanonicalRegular(path string, maximum int64) ([]byte, error) {
 		return nil, ErrUnsafeFile
 	}
 	defer file.Close()
-	return readBoundedRegularFile(file, maximum)
+	var before, after windows.ByHandleFileInformation
+	if windows.GetFileInformationByHandle(handle, &before) != nil || before.NumberOfLinks > 1 {
+		return nil, ErrUnsafeFile
+	}
+	contents, err := readBoundedRegularFile(file, maximum)
+	if err != nil {
+		return nil, ErrUnsafeFile
+	}
+	if windows.GetFileInformationByHandle(handle, &after) != nil || after.NumberOfLinks > 1 || !sameWindowsFile(before, after) {
+		return nil, ErrUnsafeFile
+	}
+	// Re-opened pathname identity is checked as well as the retained handle. This
+	// catches replacement by an ordinary local actor where share/delete policy permits it.
+	check, err := openWindowsComponent(current, false)
+	if err != nil {
+		return nil, ErrUnsafeFile
+	}
+	defer windows.CloseHandle(check)
+	var named windows.ByHandleFileInformation
+	if windows.GetFileInformationByHandle(check, &named) != nil || named.NumberOfLinks > 1 || !sameWindowsFile(before, named) {
+		return nil, ErrUnsafeFile
+	}
+	return contents, nil
 }
 
 func openWindowsComponent(path string, directory bool) (windows.Handle, error) {
@@ -81,7 +103,7 @@ func openWindowsComponent(path string, directory bool) (windows.Handle, error) {
 		windows.CloseHandle(handle)
 		return 0, err
 	}
-	if information.FileAttributes&windows.FILE_ATTRIBUTE_REPARSE_POINT != 0 ||
+	if information.NumberOfLinks > 1 || information.FileAttributes&windows.FILE_ATTRIBUTE_REPARSE_POINT != 0 ||
 		(directory && information.FileAttributes&windows.FILE_ATTRIBUTE_DIRECTORY == 0) ||
 		(!directory && information.FileAttributes&windows.FILE_ATTRIBUTE_DIRECTORY != 0) {
 		windows.CloseHandle(handle)
@@ -113,7 +135,22 @@ func writeCanonicalExclusive(path string, contents []byte, mode fs.FileMode) err
 	if _, err := f.Write(contents); err != nil {
 		return ErrUnsafeFile
 	}
-	return f.Sync()
+	if err := f.Sync(); err != nil {
+		return ErrUnsafeFile
+	}
+	var opened, named windows.ByHandleFileInformation
+	if windows.GetFileInformationByHandle(h, &opened) != nil || opened.NumberOfLinks != 1 {
+		return ErrUnsafeFile
+	}
+	check, err := openWindowsComponent(path, false)
+	if err != nil {
+		return ErrUnsafeFile
+	}
+	defer windows.CloseHandle(check)
+	if windows.GetFileInformationByHandle(check, &named) != nil || named.NumberOfLinks != 1 || !sameWindowsFile(opened, named) {
+		return ErrUnsafeFile
+	}
+	return nil
 }
 
 func validateCanonicalOutputPath(path string) error {
@@ -140,3 +177,7 @@ func validateCanonicalOutputPath(path string) error {
 	}
 	return nil
 }
+
+func sameWindowsFile(a, b windows.ByHandleFileInformation) bool {
+	return a.VolumeSerialNumber == b.VolumeSerialNumber && a.FileIndexHigh == b.FileIndexHigh && a.FileIndexLow == b.FileIndexLow
+}

tools/thothctl/internal/serverops/operations_test.go

@@ -294,7 +294,10 @@ func TestRemoveRejectsConfirmationForDifferentContainerIDs(t *testing.T) {
 
 func testInstallation(t *testing.T) config.Installation {
 	t.Helper()
-	root := t.TempDir()
+	root, err := filepath.EvalSymlinks(t.TempDir())
+	if err != nil {
+		t.Fatal(err)
+	}
 	project := filepath.Join(root, "project")
 	if err := os.Mkdir(project, 0o700); err != nil {
 		t.Fatal(err)

tools/thothctl/internal/workspaceops/operations.go

@@ -5,17 +5,21 @@ import (
 	"bytes"
 	"context"
 	"crypto/sha256"
+	"encoding/base64"
 	"encoding/hex"
 	"encoding/json"
 	"errors"
 	"fmt"
 	"io"
+	"reflect"
 	"regexp"
 	"strings"
+	"unicode/utf8"
 
 	"github.com/aritmolab/thothii/tools/thothctl/internal/compose"
 	"github.com/aritmolab/thothii/tools/thothctl/internal/config"
 	"github.com/aritmolab/thothii/tools/thothctl/internal/safeio"
+	"gopkg.in/yaml.v3"
 )
 
 const CodeRegistryBootstrapRecoveryConflict = "registry_bootstrap_recovery_conflict"
@@ -26,21 +30,23 @@ const (
 	maxAssumptionBytes = 256
 	maxResult          = 1 << 20
 	maxCandidate       = 700 << 10
+	maxAnnotations     = 16 << 20
 )
 
 var workspaceIDPattern = regexp.MustCompile(`^[a-z][a-z0-9-]{2,62}$`)
 var runIDPattern = regexp.MustCompile(`^[0-9a-f]{32}$`)
+var revisionPattern = regexp.MustCompile(`^[0-9a-f]{40}$`)
 var digestPattern = regexp.MustCompile(`^sha256:[0-9a-f]{64}$`)
 
+// Command is intentionally closed: callers cannot provide a child argv or bootstrap run ID.
 type Command interface{ workspaceCommand() }
 type InspectCommand struct {
 	WorkspaceID string
 	JSON        bool
 }
 type DwhRequest struct {
-	WorkspaceID string
-	Resume      string
-	JSON        bool
+	WorkspaceID, Resume string
+	JSON                bool
 }
 type SuggestFksRequest struct {
 	WorkspaceID string
@@ -50,11 +56,8 @@ type SuggestFksRequest struct {
 	JSON        bool
 }
 type CheckSchemaRequest struct {
-	WorkspaceID        string
-	Resume             string
-	Annotations        string
-	ReviewedCandidates string
-	JSON               bool
+	WorkspaceID, Resume, Annotations, ReviewedCandidates string
+	JSON                                                 bool
 }
 type IndexSchemaRequest struct {
 	WorkspaceID string
@@ -67,9 +70,8 @@ type EvidenceRequest struct {
 	JSON        bool
 }
 type RunRequest struct {
-	WorkspaceID string
-	Resume      string
-	JSON        bool
+	WorkspaceID, Resume string
+	JSON                bool
 }
 
 func (InspectCommand) workspaceCommand()     {}
@@ -99,6 +101,33 @@ type ArtifactIdentity struct {
 	Kind   string `json:"kind"`
 	Digest string `json:"digest"`
 }
+type hostExport struct {
+	MediaType     string `json:"mediaType"`
+	SHA256        string `json:"sha256"`
+	ContentBase64 string `json:"contentBase64"`
+}
+
+type sqlInput struct {
+	Basename      string `json:"basename"`
+	ContentBase64 string `json:"contentBase64"`
+	SHA256        string `json:"sha256"`
+}
+type annotationInput struct {
+	Basename      string `json:"basename"`
+	ContentBase64 string `json:"contentBase64"`
+	SHA256        string `json:"sha256"`
+}
+type inputEnvelope struct {
+	SchemaVersion      int              `json:"schemaVersion"`
+	Operation          string           `json:"operation"`
+	WorkspaceID        string           `json:"workspaceId"`
+	Resume             string           `json:"resume,omitempty"`
+	SQL                []sqlInput       `json:"sql,omitempty"`
+	Assume             []string         `json:"assume,omitempty"`
+	Annotations        *annotationInput `json:"annotations,omitempty"`
+	ReviewedCandidates string           `json:"reviewedCandidates,omitempty"`
+	DryRun             bool             `json:"dryRun,omitempty"`
+}
 
 func invalid(msg string) (Command, error) { return nil, errors.New(msg) }
 func requireWorkspace(v string) error {
@@ -117,46 +146,77 @@ func one(args []string, i *int, flag string) (string, error) {
 	if *i+1 >= len(args) || strings.HasPrefix(args[*i+1], "--") {
 		return "", fmt.Errorf("%s requires a value", flag)
 	}
-	*i = *i + 1
+	*i++
 	return args[*i], nil
 }
+
 func ParseWorkspaceCommand(args []string) (Command, error) {
 	if len(args) < 2 || args[0] != "workspace" {
 		return invalid("workspace command is required")
 	}
-	area, action := args[1], ""
-	rest := args[2:]
-	if area == "preprocess" || area == "schema" {
-		if len(rest) == 0 {
-			return invalid("workspace group requires an operation")
-		}
-		action = rest[0]
-		rest = rest[1:]
-	} else {
-		action = area
-	}
-	if action != "inspect" && action != "dwh" && action != "suggest-fks" && action != "check" && action != "index-schema" && action != "evidence" && action != "run" {
-		return invalid("unknown workspace command")
+	// Parse the hierarchy before options. This prevents aliases such as workspace schema dwh.
+	path := strings.Join(args[:min(3, len(args))], " ")
+	var action string
+	var rest []string
+	switch {
+	case args[1] == "inspect":
+		action = "inspect"
+		rest = args[2:]
+	case len(args) >= 3 && args[1] == "preprocess" && (args[2] == "dwh" || args[2] == "evidence" || args[2] == "run"):
+		action = "preprocess " + args[2]
+		rest = args[3:]
+	case len(args) >= 3 && args[1] == "schema" && (args[2] == "suggest-fks" || args[2] == "check"):
+		action = "schema " + args[2]
+		rest = args[3:]
+	case args[1] == "index-schema":
+		action = "index-schema"
+		rest = args[2:]
+	default:
+		return invalid("unknown workspace command: " + path)
 	}
 	var ws, resume, annotations, reviewed, output string
 	var jsonOut, dry bool
 	var sql, assume []string
 	seen := map[string]bool{}
+	allowed := func(flag string) bool {
+		switch action {
+		case "inspect":
+			return flag == "--workspace" || flag == "--json"
+		case "preprocess dwh", "preprocess run":
+			return flag == "--workspace" || flag == "--resume" || flag == "--json"
+		case "preprocess evidence":
+			return flag == "--workspace" || flag == "--resume" || flag == "--dry-run" || flag == "--json"
+		case "schema suggest-fks":
+			return flag == "--workspace" || flag == "--from-sql" || flag == "--assume" || flag == "--output" || flag == "--json"
+		case "schema check":
+			return flag == "--workspace" || flag == "--resume" || flag == "--annotations" || flag == "--reviewed-candidates" || flag == "--json"
+		case "index-schema":
+			return flag == "--workspace" || flag == "--json"
+		}
+		return false
+	}
 	for i := 0; i < len(rest); i++ {
 		f := rest[i]
-		if f == "--json" {
+		if !allowed(f) {
+			return invalid("unknown or invalid workspace option")
+		}
+		if f == "--json" || f == "--dry-run" {
 			if seen[f] {
-				return invalid("duplicate --json")
+				return invalid("duplicate " + f)
 			}
 			seen[f] = true
-			jsonOut = true
+			if f == "--json" {
+				jsonOut = true
+			} else {
+				dry = true
+			}
 			continue
 		}
+		if seen[f] && f != "--from-sql" && f != "--assume" {
+			return invalid("duplicate " + f)
+		}
 		switch f {
 		case "--workspace":
-			if seen[f] {
-				return invalid("duplicate --workspace")
-			}
 			seen[f] = true
 			v, e := one(rest, &i, f)
 			if e != nil {
@@ -164,9 +224,6 @@ func ParseWorkspaceCommand(args []string) (Command, error) {
 			}
 			ws = v
 		case "--resume":
-			if seen[f] {
-				return invalid("duplicate --resume")
-			}
 			seen[f] = true
 			v, e := one(rest, &i, f)
 			if e != nil {
@@ -174,9 +231,6 @@ func ParseWorkspaceCommand(args []string) (Command, error) {
 			}
 			resume = v
 		case "--from-sql":
-			if action != "suggest-fks" {
-				return invalid("--from-sql is valid only for schema suggest-fks")
-			}
 			v, e := one(rest, &i, f)
 			if e != nil {
 				return nil, e
@@ -186,9 +240,6 @@ func ParseWorkspaceCommand(args []string) (Command, error) {
 			}
 			sql = append(sql, v)
 		case "--assume":
-			if action != "suggest-fks" {
-				return invalid("--assume is valid only for schema suggest-fks")
-			}
 			v, e := one(rest, &i, f)
 			if e != nil {
 				return nil, e
@@ -196,14 +247,11 @@ func ParseWorkspaceCommand(args []string) (Command, error) {
 			if len(assume) >= maxAssumptions || len([]byte(v)) > maxAssumptionBytes {
 				return invalid("--assume exceeds limit")
 			}
+			if !regexp.MustCompile(`^[A-Za-z_][A-Za-z0-9_]*(?:\.[A-Za-z_][A-Za-z0-9_]*)?=[A-Za-z_][A-Za-z0-9_]*(?:\.[A-Za-z_][A-Za-z0-9_]*)?$`).MatchString(v) {
+				return invalid("--assume must be column=table")
+			}
 			assume = append(assume, v)
 		case "--output":
-			if action != "suggest-fks" {
-				return invalid("--output is valid only for schema suggest-fks")
-			}
-			if seen[f] {
-				return invalid("duplicate --output")
-			}
 			seen[f] = true
 			v, e := one(rest, &i, f)
 			if e != nil {
@@ -211,12 +259,6 @@ func ParseWorkspaceCommand(args []string) (Command, error) {
 			}
 			output = v
 		case "--annotations":
-			if action != "check" {
-				return invalid("--annotations is valid only for schema check")
-			}
-			if seen[f] {
-				return invalid("duplicate --annotations")
-			}
 			seen[f] = true
 			v, e := one(rest, &i, f)
 			if e != nil {
@@ -224,46 +266,26 @@ func ParseWorkspaceCommand(args []string) (Command, error) {
 			}
 			annotations = v
 		case "--reviewed-candidates":
-			if action != "check" {
-				return invalid("--reviewed-candidates is valid only for schema check")
-			}
-			if seen[f] {
-				return invalid("duplicate --reviewed-candidates")
-			}
 			seen[f] = true
 			v, e := one(rest, &i, f)
 			if e != nil {
 				return nil, e
 			}
 			reviewed = v
-		case "--dry-run":
-			if action != "evidence" {
-				return invalid("--dry-run is valid only for evidence")
-			}
-			if seen[f] {
-				return invalid("duplicate --dry-run")
-			}
-			seen[f] = true
-			dry = true
-		default:
-			return invalid("unknown workspace option")
 		}
 	}
 	if err := requireWorkspace(ws); err != nil {
 		return nil, err
 	}
-	if action != "inspect" && resume != "" {
+	if resume != "" {
 		if err := requireRun(resume); err != nil {
 			return nil, err
 		}
 	}
-	if resume != "" && action != "dwh" && action != "evidence" && action != "run" && action != "check" {
-		return invalid("--resume is not valid for this workspace command")
-	}
 	if action == "inspect" && resume != "" {
 		return invalid("inspect does not accept --resume")
 	}
-	if action == "check" {
+	if action == "schema check" {
 		if resume == "" {
 			return invalid("schema check requires --resume")
 		}
@@ -274,43 +296,32 @@ func ParseWorkspaceCommand(args []string) (Command, error) {
 			return invalid("--reviewed-candidates must be sha256:<hex>")
 		}
 	}
-	if action != "suggest-fks" && (len(sql) > 0 || len(assume) > 0 || output != "") {
-		return invalid("schema options are valid only for suggest-fks")
+	if action != "schema check" && (annotations != "" || reviewed != "") {
+		return invalid("annotation options are valid only for schema check")
 	}
 	switch action {
 	case "inspect":
 		return InspectCommand{ws, jsonOut}, nil
-	case "dwh":
+	case "preprocess dwh":
 		return DwhRequest{ws, resume, jsonOut}, nil
-	case "suggest-fks":
+	case "schema suggest-fks":
 		return SuggestFksRequest{ws, sql, assume, output, jsonOut}, nil
-	case "check":
+	case "schema check":
 		return CheckSchemaRequest{ws, resume, annotations, reviewed, jsonOut}, nil
 	case "index-schema":
 		return IndexSchemaRequest{ws, jsonOut}, nil
-	case "evidence":
+	case "preprocess evidence":
 		return EvidenceRequest{ws, dry, resume, jsonOut}, nil
 	default:
 		return RunRequest{ws, resume, jsonOut}, nil
 	}
 }
-
-type inputEnvelope struct {
-	SchemaVersion      int        `json:"schemaVersion"`
-	Operation          string     `json:"operation"`
-	WorkspaceID        string     `json:"workspaceId"`
-	Resume             string     `json:"resume,omitempty"`
-	SQL                []sqlInput `json:"sql,omitempty"`
-	Assume             []string   `json:"assume,omitempty"`
-	Annotations        string     `json:"annotations,omitempty"`
-	ReviewedCandidates string     `json:"reviewedCandidates,omitempty"`
-	DryRun             bool       `json:"dryRun,omitempty"`
+func min(a, b int) int {
+	if a < b {
+		return a
+	}
+	return b
 }
-type sqlInput struct {
-	Name    string `json:"name"`
-	Content string `json:"content"`
-}
-
 func operationName(c Command) string {
 	switch c.(type) {
 	case InspectCommand:
@@ -329,114 +340,275 @@ func operationName(c Command) string {
 		return "run"
 	}
 }
-func Run(ctx context.Context, installation config.Installation, runner compose.Runner, command Command, stdin io.Reader) (Result, error) {
-	env := inputEnvelope{SchemaVersion: 1, Operation: operationName(command)}
-	var outputPath string
-	switch c := command.(type) {
+
+func makeInput(c Command) (inputEnvelope, string, error) {
+	env := inputEnvelope{SchemaVersion: 1, Operation: operationName(c)}
+	var out string
+	switch x := c.(type) {
 	case InspectCommand:
-		env.WorkspaceID = c.WorkspaceID
+		env.WorkspaceID = x.WorkspaceID
 	case DwhRequest:
-		env.WorkspaceID, env.Resume = c.WorkspaceID, c.Resume
+		env.WorkspaceID, env.Resume = x.WorkspaceID, x.Resume
 	case SuggestFksRequest:
-		env.WorkspaceID, env.Assume, outputPath = c.WorkspaceID, c.Assume, c.Output
-		if outputPath != "" {
-			if err := safeio.ValidateCanonicalOutputPath(outputPath); err != nil {
-				return Result{}, errors.New("unsafe output file")
+		env.WorkspaceID, env.Assume, out = x.WorkspaceID, x.Assume, x.Output
+		if out != "" {
+			if err := safeio.ValidateCanonicalOutputPath(out); err != nil {
+				return env, "", errors.New("unsafe output file")
 			}
 		}
 		var total int64
-		for _, path := range c.FromSQL {
+		for _, path := range x.FromSQL {
 			b, e := safeio.ReadCanonicalUTF8(path, maxSQLFile)
 			if e != nil {
-				return Result{}, errors.New("unsafe SQL input")
+				return env, "", errors.New("unsafe SQL input")
 			}
 			total += int64(len(b))
 			if total > maxSQLTotal {
-				return Result{}, errors.New("SQL input exceeds limit")
-			}
-			env.SQL = append(env.SQL, sqlInput{path, string(b)})
-		}
-		if len(env.SQL) > 0 {
-			var n int
-			for _, x := range env.SQL {
-				n += len(x.Content)
-			}
-			if n > maxCandidate {
-				return Result{}, errors.New("candidate input exceeds limit")
+				return env, "", errors.New("SQL input exceeds limit")
 			}
+			base := path[strings.LastIndexAny(path, "/\\")+1:]
+			env.SQL = append(env.SQL, sqlInput{base, base64.StdEncoding.EncodeToString(b), DigestBytes(b)})
 		}
 	case CheckSchemaRequest:
-		env.WorkspaceID, env.Resume, env.Annotations, env.ReviewedCandidates = c.WorkspaceID, c.Resume, c.Annotations, c.ReviewedCandidates
-		if c.Annotations != "" {
-			b, e := safeio.ReadCanonicalUTF8(c.Annotations, 16<<20)
+		env.WorkspaceID, env.Resume, env.ReviewedCandidates = x.WorkspaceID, x.Resume, x.ReviewedCandidates
+		if x.Annotations != "" {
+			b, e := safeio.ReadCanonicalUTF8(x.Annotations, maxAnnotations)
 			if e != nil {
-				return Result{}, errors.New("unsafe annotation input")
+				return env, "", errors.New("unsafe annotation input")
 			}
-			env.Annotations = string(b)
+			base := x.Annotations[strings.LastIndexAny(x.Annotations, "/\\")+1:]
+			env.Annotations = &annotationInput{base, base64.StdEncoding.EncodeToString(b), DigestBytes(b)}
 		}
 	case IndexSchemaRequest:
-		env.WorkspaceID = c.WorkspaceID
+		env.WorkspaceID = x.WorkspaceID
 	case EvidenceRequest:
-		env.WorkspaceID, env.Resume, env.DryRun = c.WorkspaceID, c.Resume, c.DryRun
+		env.WorkspaceID, env.Resume, env.DryRun = x.WorkspaceID, x.Resume, x.DryRun
 	case RunRequest:
-		env.WorkspaceID, env.Resume = c.WorkspaceID, c.Resume
+		env.WorkspaceID, env.Resume = x.WorkspaceID, x.Resume
 	default:
-		return Result{}, errors.New("unsupported workspace command")
+		return env, "", errors.New("unsupported workspace command")
 	}
 	payload, e := json.Marshal(env)
+	if e != nil {
+		return env, "", e
+	}
+	if len(payload) > maxResult {
+		return env, "", errors.New("request exceeds limit")
+	}
+	return env, string(payload), nil
+}
+
+var commonIngress = map[string]bool{"schemaVersion": true, "operation": true, "workspaceId": true}
+
+func validateIngress(payload []byte, expected inputEnvelope) error {
+	var raw map[string]json.RawMessage
+	d := json.NewDecoder(bytes.NewReader(payload))
+	d.UseNumber()
+	if d.Decode(&raw) != nil {
+		return errors.New("invalid workspace request")
+	}
+	var extra any
+	if d.Decode(&extra) != io.EOF {
+		return errors.New("invalid workspace request")
+	}
+	var supplied inputEnvelope
+	dec := json.NewDecoder(bytes.NewReader(payload))
+	dec.DisallowUnknownFields()
+	if dec.Decode(&supplied) != nil || supplied.SchemaVersion != 1 || supplied.Operation != expected.Operation || supplied.WorkspaceID != expected.WorkspaceID {
+		return errors.New("invalid workspace request")
+	}
+	if !reflect.DeepEqual(supplied, expected) {
+		return errors.New("workspace request does not match command")
+	}
+	allowed := map[string]bool{}
+	for k := range commonIngress {
+		allowed[k] = true
+	}
+	switch expected.Operation {
+	case "dwh", "run":
+		if expected.Resume != "" {
+			allowed["resume"] = true
+		}
+	case "evidence":
+		allowed["resume"] = true
+		allowed["dryRun"] = true
+	case "suggest-fks":
+		allowed["sql"] = true
+		allowed["assume"] = true
+	case "check":
+		allowed["resume"] = true
+		allowed["annotations"] = true
+		allowed["reviewedCandidates"] = true
+	}
+	for k := range raw {
+		if !allowed[k] {
+			return errors.New("invalid workspace request")
+		}
+	}
+	return nil
+}
+
+func Run(ctx context.Context, installation config.Installation, runner compose.Runner, command Command, stdin io.Reader) (Result, error) {
+	env, generated, e := makeInput(command)
 	if e != nil {
 		return Result{}, e
 	}
+	payload := []byte(generated)
 	if stdin != nil {
-		payload, e = io.ReadAll(io.LimitReader(stdin, 1<<20+1))
-		if e != nil {
-			return Result{}, e
-		}
-		if len(payload) > 1<<20 {
+		payload, e = io.ReadAll(io.LimitReader(stdin, maxResult+1))
+		if e != nil || len(payload) > maxResult {
 			return Result{}, errors.New("request exceeds limit")
 		}
-		var supplied inputEnvelope
-		d := json.NewDecoder(bytes.NewReader(payload))
-		d.DisallowUnknownFields()
-		if e = d.Decode(&supplied); e != nil || supplied.SchemaVersion != 1 || supplied.Operation != env.Operation || supplied.WorkspaceID != env.WorkspaceID {
-			return Result{}, errors.New("invalid workspace request")
+		if e = validateIngress(payload, env); e != nil {
+			return Result{}, e
 		}
 	}
-
-	args := installation.ComposeArgs("run", "--rm", "--no-deps", "workspace-maintenance", "--operation", operationName(command), "--workspace", env.WorkspaceID)
-	cr, runErr := runner.RunBounded(ctx, args, bytes.NewReader(payload), compose.CaptureLimits{StdoutBytes: 1 << 20, StderrBytes: 64 << 10})
-	if runErr != nil && (errors.Is(runErr, compose.ErrOutputLimit) || cr.Stdout == "") {
+	args := installation.ComposeArgs("run", "--rm", "--no-deps", "--no-TTY", "workspace-maintenance", "--operation", operationName(command), "--workspace", env.WorkspaceID)
+	cr, runErr := runner.RunBounded(ctx, args, bytes.NewReader(payload), compose.CaptureLimits{StdoutBytes: maxResult, StderrBytes: 64 << 10})
+	if errors.Is(runErr, compose.ErrOutputLimit) {
 		return Result{}, runErr
 	}
+	if len(cr.Stdout) == 0 {
+		return Result{}, runErrOr(runErr, "workspace maintenance returned no result")
+	}
 	if len(cr.Stdout) > maxResult {
 		return Result{}, errors.New("invalid workspace result")
 	}
-	var result Result
-	dec := json.NewDecoder(strings.NewReader(cr.Stdout))
-	dec.DisallowUnknownFields()
-	if e := dec.Decode(&result); e != nil {
+	var raw map[string]json.RawMessage
+	d := json.NewDecoder(strings.NewReader(cr.Stdout))
+	if d.Decode(&raw) != nil {
 		return Result{}, errors.New("invalid workspace result")
 	}
 	var extra any
-	if e := dec.Decode(&extra); e != io.EOF {
+	if d.Decode(&extra) != io.EOF {
 		return Result{}, errors.New("invalid workspace result")
 	}
-	if result.SchemaVersion != 1 || result.WorkspaceID != env.WorkspaceID || result.Operation != operationName(command) || !validStatus(result.Status) || !validCode(result.Code) {
+	var export *hostExport
+	hasExport := false
+	if h, ok := raw["hostExport"]; ok {
+		hasExport = true
+		if operationName(command) != "suggest-fks" {
+			return Result{}, errors.New("invalid workspace result")
+		}
+		if json.Unmarshal(h, &export) != nil {
+			return Result{}, errors.New("invalid host export")
+		}
+		delete(raw, "hostExport")
+	}
+	b, _ := json.Marshal(raw)
+	var result Result
+	dec := json.NewDecoder(bytes.NewReader(b))
+	dec.DisallowUnknownFields()
+	if dec.Decode(&result) != nil {
 		return Result{}, errors.New("invalid workspace result")
 	}
-	if outputPath != "" {
-		if len(cr.Stdout) > maxCandidate {
-			return Result{}, errors.New("candidate export exceeds limit")
-		}
-		if err := safeio.WriteCanonicalExclusive(outputPath, []byte(cr.Stdout), 0o600); err != nil {
-			return Result{}, errors.New("unsafe output file")
+	if e = validateResult(result, env.WorkspaceID, operationName(command)); e != nil {
+		return Result{}, e
+	}
+	if runErr != nil {
+		if result.Status == "blocked" && cr.ExitCode == 3 {
+		} else if result.Status == "failed" && cr.ExitCode == 1 {
+		} else {
+			return Result{}, runErr
 		}
 	}
-
+	if hasExport {
+		if export == nil {
+			return Result{}, errors.New("invalid candidate export")
+		}
+		if !candidateBoundToResult(*export, result) {
+			return Result{}, errors.New("invalid candidate identity")
+		}
+		if err := publishCandidate(export, result, outPath(command)); err != nil {
+			return Result{}, err
+		}
+	} else if outPath(command) != "" {
+		return Result{}, errors.New("candidate export is required")
+	}
 	return result, nil
 }
-func DigestBytes(b []byte) string { s := sha256.Sum256(b); return "sha256:" + hex.EncodeToString(s[:]) }
+func runErrOr(e error, msg string) error {
+	if e != nil {
+		return e
+	}
+	return errors.New(msg)
+}
+func outPath(c Command) string {
+	if x, ok := c.(SuggestFksRequest); ok {
+		return x.Output
+	}
+	return ""
+}
+func candidateBoundToResult(x hostExport, result Result) bool {
+	if result.RunID == "" {
+		return false
+	}
+	for _, artifact := range result.ArtifactIdentities {
+		if artifact.Kind == "fk-candidates" && artifact.Digest == x.SHA256 {
+			return true
+		}
+	}
+	return false
+}
 
+func publishCandidate(x *hostExport, result Result, path string) error {
+	if path == "" {
+		return nil
+	}
+	if x.MediaType != "application/yaml" && x.MediaType != "text/yaml" {
+		return errors.New("invalid candidate export")
+	}
+	if !digestPattern.MatchString(x.SHA256) {
+		return errors.New("invalid candidate export")
+	}
+	b, e := base64.StdEncoding.DecodeString(x.ContentBase64)
+	if e != nil || len(b) > maxCandidate || !utf8.Valid(b) {
+		return errors.New("invalid candidate export")
+	}
+	if DigestBytes(b) != x.SHA256 {
+		return errors.New("invalid candidate export")
+	}
+	var doc any
+	if yaml.Unmarshal(b, &doc) != nil {
+		return errors.New("invalid candidate export")
+	}
+	if result.RunID == "" || !runIDPattern.MatchString(result.RunID) {
+		return errors.New("invalid candidate identity")
+	}
+	if e = safeio.WriteCanonicalExclusive(path, b, 0o600); e != nil {
+		return errors.New("unsafe output file")
+	}
+	return nil
+}
+func validateResult(r Result, workspace, operation string) error {
+	if r.SchemaVersion != 1 || r.WorkspaceID != workspace || r.Operation != operation || !validStatus(r.Status) || !validCode(r.Code) || !revisionPattern.MatchString(r.WorkspaceRevision) || !revisionPattern.MatchString(r.DescriptorBlob) {
+		return errors.New("invalid workspace result")
+	}
+	if r.RunID != "" && !runIDPattern.MatchString(r.RunID) {
+		return errors.New("invalid workspace result")
+	}
+	for k, v := range r.ChildRuns {
+		if k == "" || !runIDPattern.MatchString(v) {
+			return errors.New("invalid workspace result")
+		}
+	}
+	for _, a := range r.ArtifactIdentities {
+		if a.Kind == "" || !digestPattern.MatchString(a.Digest) {
+			return errors.New("invalid workspace result")
+		}
+	}
+	if r.CompletedStages == nil {
+		return errors.New("invalid workspace result")
+	}
+	if r.Status == "blocked" && (r.Code != "manual_review_required" && r.Code != "evidence_materialization_required" && r.Code != "preprocessing_conflict" && r.Code != "preprocessing_resume_mismatch" && r.Code != CodeRegistryBootstrapRecoveryConflict) {
+		return errors.New("invalid workspace result")
+	}
+	if r.Status != "blocked" && r.Code == CodeRegistryBootstrapRecoveryConflict {
+		return errors.New("invalid workspace result")
+	}
+	return nil
+}
+func DigestBytes(b []byte) string { s := sha256.Sum256(b); return "sha256:" + hex.EncodeToString(s[:]) }
 func validStatus(v string) bool {
 	switch v {
 	case "succeeded", "unchanged", "dry_run", "blocked", "failed":

tools/thothctl/internal/workspaceops/operations_test.go

@@ -1,8 +1,16 @@
 package workspaceops
 
 import (
+	"encoding/base64"
+	"os"
+	"path/filepath"
 	"reflect"
+	"strings"
 	"testing"
+
+	"context"
+	"github.com/aritmolab/thothii/tools/thothctl/internal/compose"
+	"github.com/aritmolab/thothii/tools/thothctl/internal/config"
 )
 
 func TestParseWorkspaceCommands(t *testing.T) {
@@ -48,3 +56,79 @@ func TestParseWorkspaceRejectsUnsafeOrAmbiguousOptions(t *testing.T) {
 		}
 	}
 }
+
+func TestParseWorkspaceRejectsNonContractHierarchyAndAssumeShell(t *testing.T) {
+	for _, argv := range [][]string{
+		{"workspace", "schema", "dwh", "--workspace", "psd"},
+		{"workspace", "preprocess", "check", "--workspace", "psd"},
+		{"workspace", "suggest-fks", "--workspace", "psd"},
+		{"workspace", "inspect", "--workspace", "psd", "--bootstrap-run-id", strings.Repeat("a", 32)},
+		{"workspace", "schema", "suggest-fks", "--workspace", "psd", "--assume", "a"},
+		{"workspace", "schema", "suggest-fks", "--workspace", "psd", "--assume", "a=$(id)"},
+	} {
+		if _, err := ParseWorkspaceCommand(argv); err == nil {
+			t.Errorf("accepted non-contract argv %v", argv)
+		}
+	}
+}
+
+func TestRunUsesBase64BasenameIngressAndNoTTY(t *testing.T) {
+	root, err := filepath.EvalSymlinks(t.TempDir())
+	if err != nil {
+		t.Fatal(err)
+	}
+	sqlPath := filepath.Join(root, "schema.sql")
+	if err := os.WriteFile(sqlPath, []byte("select 1"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	out := filepath.Join(root, "candidate.yaml")
+	resultJSON := `{"schemaVersion":1,"status":"succeeded","code":"ok","workspaceId":"psd","workspaceRevision":"0123456789012345678901234567890123456789","descriptorBlob":"abcdefabcdefabcdefabcdefabcdefabcdefabcd","operation":"suggest-fks","runId":"0123456789abcdef0123456789abcdef","completedStages":[]}`
+	script := "#!/bin/sh\ncat >/dev/null\nprintf '%s' '" + resultJSON + "'\n"
+	fake := filepath.Join(root, "docker")
+	if err := os.WriteFile(fake, []byte(script), 0o700); err != nil {
+		t.Fatal(err)
+	}
+	cmd, err := ParseWorkspaceCommand([]string{"workspace", "schema", "suggest-fks", "--workspace", "psd", "--from-sql", sqlPath})
+	if err != nil {
+		t.Fatal(err)
+	}
+	got, err := Run(context.Background(), config.Installation{ProjectDirectory: root, EnvFile: filepath.Join(root, "env")}, compose.NewRunner(fake), cmd, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if got.Code != "ok" {
+		t.Fatalf("result = %#v", got)
+	}
+	_ = out
+}
+
+func TestRunPublishesOnlyVerifiedCandidateExport(t *testing.T) {
+	root, err := filepath.EvalSymlinks(t.TempDir())
+	if err != nil {
+		t.Fatal(err)
+	}
+	candidate := []byte("candidates: []\n")
+	digest := DigestBytes(candidate)
+	encoded := base64.StdEncoding.EncodeToString(candidate)
+	resultJSON := `{"schemaVersion":1,"status":"succeeded","code":"ok","workspaceId":"psd","workspaceRevision":"0123456789012345678901234567890123456789","descriptorBlob":"abcdefabcdefabcdefabcdefabcdefabcdefabcd","operation":"suggest-fks","runId":"0123456789abcdef0123456789abcdef","completedStages":[],"artifactIdentities":[{"kind":"fk-candidates","digest":"` + digest + `"}],"hostExport":{"mediaType":"application/yaml","sha256":"` + digest + `","contentBase64":"` + encoded + `"}}`
+	fake := filepath.Join(root, "docker")
+	if err := os.WriteFile(fake, []byte("#!/bin/sh\ncat >/dev/null\nprintf '%s' '"+resultJSON+"'\n"), 0o700); err != nil {
+		t.Fatal(err)
+	}
+	path := filepath.Join(root, "out.yaml")
+	cmd, err := ParseWorkspaceCommand([]string{"workspace", "schema", "suggest-fks", "--workspace", "psd", "--output", path})
+	if err != nil {
+		t.Fatal(err)
+	}
+	got, err := Run(context.Background(), config.Installation{ProjectDirectory: root, EnvFile: filepath.Join(root, "env")}, compose.NewRunner(fake), cmd, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if got.RunID == "" {
+		t.Fatal("missing run identity")
+	}
+	b, err := os.ReadFile(path)
+	if err != nil || string(b) != string(candidate) {
+		t.Fatalf("candidate = %q, %v", b, err)
+	}
+}