Resolve check and freshen paths against the manifest's directory (closes #177)

Without --base, check and freshen now look for a manifest's files in the
directory that holds the manifest, the file named or the one found in a
directory argument, instead of the current directory. check of a manifest
given by URL still uses the current directory, and a --base given on the
command line, the current directory included, still overrides. The --base
help text of both commands and the README's Tool Examples state the
default; the README gains a freshen entry to do so.

Model: opus-5-5

internal/cli/check.go

@@ -299,6 +299,17 @@ func (mfa *CLIApp) checkManifestOperation(
 		return fmt.Errorf("check: %w", err)
 	}
 
+	// Without --base, the manifest's paths are resolved against the
+	// directory holding it, or the current directory for a manifest URL.
+	basePath := "."
+
+	switch {
+	case cmd.IsSet(flagBase):
+		basePath = cmd.String(flagBase)
+	case !isHTTPURL(manifestPath):
+		basePath = filepath.Dir(manifestPath)
+	}
+
 	// URL manifests need to be downloaded to a temp file for the checker
 	if isHTTPURL(manifestPath) {
 		tmpPath, tmpErr := mfa.fetchManifestToTemp(ctx, manifestPath)
@@ -311,7 +322,6 @@ func (mfa *CLIApp) checkManifestOperation(
 		manifestPath = tmpPath
 	}
 
-	basePath := cmd.String("base")
 	showProgress := cmd.Bool("progress")
 
 	log.Infof("checking manifest %s with base %s", manifestPath, basePath)

internal/cli/entry_test.go

@@ -8,6 +8,7 @@ import (
 	"fmt"
 	"io"
 	"math/rand"
+	"net/http/httptest"
 	"os"
 	"path/filepath"
 	"slices"
@@ -979,6 +980,83 @@ func TestCheckNeverReportsManifest(t *testing.T) {
 	}
 }
 
+// setupManifestInSubdir makes a temp dir holding a.txt and sub/b.txt, where
+// sub/index.mf is the manifest gen writes for sub, and makes it the working
+// directory, so a test calling it cannot run in parallel. It returns the
+// temp dir.
+func setupManifestInSubdir(t *testing.T) string {
+	t.Helper()
+
+	root := t.TempDir()
+	sub := filepath.Join(root, "sub")
+
+	fs := afero.NewOsFs()
+	require.NoError(t, fs.MkdirAll(sub, 0o750))
+	writeTestFile(t, fs, filepath.Join(root, "a.txt"), "not in the manifest")
+	writeTestFile(t, fs, filepath.Join(sub, "b.txt"), "in the manifest")
+
+	opts := testOpts([]string{
+		testApp, cmdGenerate, "-q", "-o", filepath.Join(sub, defaultManifestName), sub,
+	}, fs)
+	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+	t.Chdir(root)
+
+	return root
+}
+
+// TestCheckResolvesEntriesAgainstManifestDirectory runs check from the
+// directory above sub, on the manifest in sub. Without --base, the
+// manifest's entries are looked for in sub, whether check is given the
+// manifest or sub, and the files above sub are not reported. --base names
+// the directory to look in instead, the current one included.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestCheckResolvesEntriesAgainstManifestDirectory(t *testing.T) {
+	root := setupManifestInSubdir(t)
+
+	for _, tc := range []struct {
+		args     []string
+		exitCode int
+		failure  string // a line check must print, if any
+	}{
+		{[]string{"sub"}, 0, ""},
+		{[]string{"sub/index.mf"}, 0, ""},
+		{[]string{filepath.Join(root, "sub")}, 0, ""},
+		{[]string{testFlagBase, "sub", "sub/index.mf"}, 0, ""},
+		{[]string{testFlagBase, ".", "sub/index.mf"}, 1, "MISSING: b.txt"},
+	} {
+		t.Run(strings.Join(tc.args, " "), func(t *testing.T) {
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdCheck, testFlagNoExtra}, tc.args,
+			), afero.NewOsFs())
+			assert.Equal(t, tc.exitCode, runCLI(opts), "stderr: %s", testStderr(t, opts))
+			assert.Contains(t, testStderr(t, opts), tc.failure)
+		})
+	}
+}
+
+// TestCheckURLManifestResolvesEntriesAgainstCurrentDirectory runs check on
+// a manifest given by URL, from a directory holding the file it lists: the
+// file is looked for there.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestCheckURLManifestResolvesEntriesAgainstCurrentDirectory(t *testing.T) {
+	files := map[string][]byte{testFileTxt: []byte("hello")}
+
+	server := httptest.NewServer(fetchTestHandler(manifestOf(t, files), files))
+	defer server.Close()
+
+	cwd := chdirTemp(t)
+	require.NoError(t,
+		os.WriteFile(filepath.Join(cwd, testFileTxt), files[testFileTxt], 0o600))
+
+	opts := testOpts([]string{
+		testApp, cmdCheck, testFlagNoExtra, server.URL + "/" + defaultManifestName,
+	}, afero.NewOsFs())
+	assert.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+}
+
 // unlistableDirFs is a filesystem on which one directory cannot be listed.
 type unlistableDirFs struct {
 	afero.Fs

internal/cli/freshen.go

@@ -497,7 +497,6 @@ func (mfa *CLIApp) freshenManifestOperation(
 ) error {
 	log.Debug("freshenManifestOperation()")
 
-	basePath := cmd.String("base")
 	showProgress := cmd.Bool("progress")
 
 	// Find manifest file
@@ -506,6 +505,13 @@ func (mfa *CLIApp) freshenManifestOperation(
 		return fmt.Errorf("freshen: %w", err)
 	}
 
+	// Without --base, the manifest's paths are resolved against the
+	// directory holding it.
+	basePath := filepath.Dir(manifestPath)
+	if cmd.IsSet(flagBase) {
+		basePath = cmd.String(flagBase)
+	}
+
 	//nolint:contextcheck // mfer loads a manifest without a context
 	existingByPath, err := mfa.loadExistingEntries(manifestPath)
 	if err != nil {

internal/cli/freshen_test.go

@@ -7,6 +7,7 @@ import (
 	"os"
 	"path/filepath"
 	"slices"
+	"strings"
 	"testing"
 	"time"
 
@@ -300,6 +301,41 @@ func TestFreshenLeavesLeftoverTempFileOutOfListing(t *testing.T) {
 		manifestPaths(t, fs, manifestPath))
 }
 
+// TestFreshenResolvesEntriesAgainstManifestDirectory adds sub/c.txt, then
+// runs freshen from the directory above sub, on the manifest in sub.
+// Without --base, the manifest then lists the files in sub, whether freshen
+// is given the manifest or sub. --base names the directory to list instead,
+// the current one included.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFreshenResolvesEntriesAgainstManifestDirectory(t *testing.T) {
+	for _, tc := range []struct {
+		args []string
+		want []string // the paths the manifest lists afterwards
+	}{
+		{[]string{"sub"}, []string{"b.txt", "c.txt"}},
+		{[]string{"sub/index.mf"}, []string{"b.txt", "c.txt"}},
+		{
+			[]string{testFlagBase, ".", "sub/index.mf"},
+			[]string{"a.txt", "sub/b.txt", "sub/c.txt"},
+		},
+	} {
+		t.Run(strings.Join(tc.args, " "), func(t *testing.T) {
+			fs := afero.NewOsFs()
+			root := setupManifestInSubdir(t)
+			writeTestFile(t, fs, filepath.Join(root, "sub", "c.txt"), "added")
+
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdFreshen, "-q"}, tc.args,
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assert.ElementsMatch(t, tc.want, manifestPaths(t, fs,
+				filepath.Join(root, "sub", defaultManifestName)))
+		})
+	}
+}
+
 // TestFreshenRecordEntryMtimePresence pins the behavior of recordEntry
 // with respect to MFFilePath.Mtime, which is a message pointer with
 // proto3 field presence and may legitimately be absent.

internal/cli/mfer.go

@@ -24,6 +24,7 @@ const (
 	cmdList     = "list"
 	cmdVersion  = "version"
 
+	flagBase               = "base"
 	flagProgress           = "progress"
 	flagTimeout            = "timeout"
 	flagDest               = "dest"
@@ -259,10 +260,11 @@ func (mfa *CLIApp) checkCommand() *cli.Command {
 		},
 		Flags: append(commonFlags(),
 			&cli.StringFlag{
-				Name:    "base",
+				Name:    flagBase,
 				Aliases: []string{"b"},
-				Value:   ".",
-				Usage:   "Base directory for resolving relative paths from manifest",
+				Usage: "Base directory for resolving relative paths from manifest " +
+					"(by default the directory holding the manifest, or the " +
+					"current directory for a manifest URL)",
 			},
 			&cli.BoolFlag{
 				Name:    flagProgress,
@@ -292,10 +294,10 @@ func (mfa *CLIApp) freshenCommand() *cli.Command {
 		},
 		Flags: append(commonFlags(),
 			&cli.StringFlag{
-				Name:    "base",
+				Name:    flagBase,
 				Aliases: []string{"b"},
-				Value:   ".",
-				Usage:   "Base directory for resolving relative paths",
+				Usage: "Base directory for resolving relative paths " +
+					"(by default the directory holding the manifest)",
 			},
 			&cli.BoolFlag{
 				Name:    "follow-symlinks",