refactor: clear cmd/ purity grandfathered map

Move BuildVault from journal/cmd/obsidian to journal/core/obsidian,
remove stale grandfathered entries (one, every already migrated).
TestCmdDirPurity now passes with zero exceptions.

Also adds gitnexus-analyze Makefile target.

Spec: specs/cmd-purity-cleanup.md
Signed-off-by: Jose Alekhinne <jose@ctx.ist>

Author: josealekhine

.context/TASKS.md

@@ -27,28 +27,34 @@ TASK STATUS LABELS:
 
 ### Misc
 
-- [ ] gitnexus analyze --embeddings --skill : we need a make target, but also this
-  butchers AGENTS.md and CLAUDE.md so those files need to be reverted and
-  GITNEXUS.md should be updated accordingly. The make target should remind
-  the user about it.
-
-- [ ] SMB mount path support: add `CTX_BACKUP_SMB_MOUNT_PATH` env var so `ctx backup` can use fstab/systemd automounts instead of requiring GVFS. Spec: specs/smb-mount-path-support.md #priority:medium #added:2026-04-04-010000
+- [ ] SMB mount path support: add `CTX_BACKUP_MOUNT_PATH` env var so 
+  `ctx backup` can use fstab/systemd automounts instead of requiring GVFS. 
+  Spec: specs/smb-mount-path-support.md #priority:medium #added:2026-04-04-010000
 
 ### Architecture Docs
 
-- [ ] Publish architecture docs to docs/: copy ARCHITECTURE.md, DETAILED_DESIGN domain files, and CHEAT-SHEETS.md to docs/reference/. Sanitize intervention points into docs/contributing/. Exclude DANGER-ZONES.md and ARCHITECTURE-PRINCIPAL.md (internal only). Spec: specs/publish-architecture-docs.md #priority:medium #added:2026-04-03-150000
+- [ ] Publish architecture docs to docs/: copy ARCHITECTURE.md, 
+  DETAILED_DESIGN domain files, and CHEAT-SHEETS.md to docs/reference/. 
+  Sanitize intervention points into docs/contributing/. 
+  Exclude DANGER-ZONES.md and ARCHITECTURE-PRINCIPAL.md (internal only). 
+  Spec: specs/publish-architecture-docs.md #priority:medium #added:2026-04-03-150000
 
-- [ ] Update ctx-architecture skill to append discovered terms to GLOSSARY.md during Phase 3. Additive only, max 10 terms per run, project-specific only, alphabetical insertion, skip if GLOSSARY.md empty. Print added terms in convergence report. Spec: specs/publish-architecture-docs.md #priority:low #added:2026-04-03-153000
+- [ ] Update ctx-architecture skill to append discovered terms to GLOSSARY.md 
+  during Phase 3. Additive only, max 10 terms per run, project-specific only, 
+  alphabetical insertion, skip if GLOSSARY.md empty. Print added terms in 
+  convergence report. Spec: specs/publish-architecture-docs.md #priority:low #added:2026-04-03-153000
 
 ### Code Cleanup Findings
 
 
-- [ ] Extend flagbind helpers (IntFlag, DurationFlag, DurationFlagP, StringP, BoolP) and migrate ~50 call sites to unblock TestNoFlagBindOutsideFlagbind #added:2026-04-01-233250
+- [x] Extend flagbind helpers (IntFlag, DurationFlag, DurationFlagP, StringP, 
+  BoolP) and migrate ~50 call sites to unblock TestNoFlagBindOutsideFlagbind 
+  #added:2026-04-01-233250
 
 - [ ] Implement journal compaction: Elastic-style tiered storage with tar.gz 
   backup. Spec: specs/journal-compact.md #added:2026-03-31-110005
 
-- [ ] Refactor 28 grandfathered cmd/ purity violations found by 
+- [x] Refactor 28 grandfathered cmd/ purity violations found by 
   TestCmdDirPurity: move unexported helpers, exported non-Cmd/Run functions, 
   and types from cmd/ directories to core/. See grandfathered map in 
   compliance_test.go for the full list. #priority:medium #added:2026-03-31-005115

Makefile

@@ -228,6 +228,11 @@ register-mcp:
 	@./hack/register-gemini-search.sh
 	@./hack/register-gitnexus.sh
 
+## gitnexus-analyze: Updates gitnexus embeddings and skill.
+gitnexus-analyze:
+	gitnexus analyze --embeddings --skill
+	echo "GitNexus updated AGENTS.md and CLAUDE.md -- DO NOT COMMIT THEM!"
+
 ## gemini-search: Register gemini-search MCP server with Claude Code
 gemini-search:
 	@./hack/register-gemini-search.sh

internal/cli/journal/cmd/obsidian/doc.go

@@ -7,7 +7,6 @@
 // Package obsidian implements the ctx journal obsidian subcommand.
 //
 // [Cmd] builds the cobra.Command with --output flag. [Run]
-// generates an Obsidian vault from journal entries with wikilinks,
-// topic pages, and frontmatter. [BuildVault] handles the file
-// generation pipeline.
+// delegates to core/obsidian.BuildVault to generate an
+// Obsidian vault from journal entries.
 package obsidian

internal/cli/journal/cmd/obsidian/run.go

@@ -7,260 +7,25 @@
 package obsidian
 
 import (
-	"fmt"
-	"os"
 	"path/filepath"
 
 	"github.com/spf13/cobra"
 
-	"github.com/ActiveMemory/ctx/internal/assets/tpl"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/consolidate"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/format"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/frontmatter"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/moc"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/parse"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/reduce"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/section"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/turn"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/wikilink"
-	"github.com/ActiveMemory/ctx/internal/cli/journal/core/wrap"
+	coreObsidian "github.com/ActiveMemory/ctx/internal/cli/journal/core/obsidian"
 	"github.com/ActiveMemory/ctx/internal/config/dir"
-	"github.com/ActiveMemory/ctx/internal/config/file"
-	"github.com/ActiveMemory/ctx/internal/config/fs"
-	"github.com/ActiveMemory/ctx/internal/config/obsidian"
-	errFs "github.com/ActiveMemory/ctx/internal/err/fs"
-	errJournal "github.com/ActiveMemory/ctx/internal/err/journal"
-	"github.com/ActiveMemory/ctx/internal/io"
 	"github.com/ActiveMemory/ctx/internal/rc"
-	"github.com/ActiveMemory/ctx/internal/write/err"
-	writeObsidian "github.com/ActiveMemory/ctx/internal/write/obsidian"
 )
 
 // Run generates an Obsidian vault from journal entries.
 //
-// Pipeline:
-//  1. Scan entries (reuse core.ScanJournalEntries)
-//  2. Create output dirs (entries/, topics/, files/, types/, .obsidian/)
-//  3. Write .obsidian/app.json
-//  4. Transform and write entries (normalize, convert links, transform
-//     frontmatter, add related footer)
-//  5. Build indices (reuse core.BuildTopicIndex etc.)
-//  6. Generate and write MOC pages
-//  7. Generate and write Home.md
-//
 // Parameters:
 //   - cmd: Cobra command for output stream
 //   - output: Output directory for the vault
 //
 // Returns:
 //   - error: Non-nil if generation fails
 func Run(cmd *cobra.Command, output string) error {
-	return BuildVault(
+	return coreObsidian.BuildVault(
 		cmd, filepath.Join(rc.ContextDir(), dir.Journal), output,
 	)
 }
-
-// BuildVault generates an Obsidian vault from journal entries in
-// journalDir and writes the output to the output directory.
-//
-// Parameters:
-//   - cmd: Cobra command for output stream
-//   - journalDir: Path to the source journal directory
-//   - output: Output directory for the vault
-//
-// Returns:
-//   - error: Non-nil if generation fails
-func BuildVault(cmd *cobra.Command, journalDir, output string) error {
-	if _, statErr := os.Stat(journalDir); os.IsNotExist(statErr) {
-		return errJournal.NoDir(journalDir)
-	}
-
-	entries, scanErr := parse.ScanJournalEntries(journalDir)
-	if scanErr != nil {
-		return errJournal.Scan(scanErr)
-	}
-
-	if len(entries) == 0 {
-		return errJournal.NoEntries(journalDir)
-	}
-
-	// Create output directory structure
-	dirs := []string{
-		output,
-		filepath.Join(output, obsidian.DirEntries),
-		filepath.Join(output, obsidian.DirConfig),
-		filepath.Join(output, dir.JournTopics),
-		filepath.Join(output, dir.JournalFiles),
-		filepath.Join(output, dir.JournalTypes),
-	}
-	for _, d := range dirs {
-		if mkErr := io.SafeMkdirAll(d, fs.PermExec); mkErr != nil {
-			return errFs.Mkdir(d, mkErr)
-		}
-	}
-
-	// Write .obsidian/app.json
-	appConfigPath := filepath.Join(
-		output, obsidian.DirConfig, obsidian.AppConfigFile,
-	)
-	if writeErr := io.SafeWriteFile(
-		appConfigPath, []byte(obsidian.AppConfig), fs.PermFile,
-	); writeErr != nil {
-		return errFs.FileWrite(appConfigPath, writeErr)
-	}
-
-	// Write README
-	readmePath := filepath.Join(output, file.Readme)
-	if writeErr := io.SafeWriteFile(
-		readmePath,
-		[]byte(fmt.Sprintf(tpl.ObsidianReadme, journalDir)),
-		fs.PermFile,
-	); writeErr != nil {
-		return errFs.FileWrite(readmePath, writeErr)
-	}
-
-	// Build indices for MOC pages and related footer
-	regularEntries := moc.FilterRegularEntries(entries)
-
-	topicEntries := moc.FilterEntriesWithTopics(entries)
-	topics := section.BuildTopicIndex(topicEntries)
-
-	keyFileEntries := moc.FilterEntriesWithKeyFiles(entries)
-	keyFiles := section.BuildKeyFileIndex(keyFileEntries)
-
-	typeEntries := moc.FilterEntriesWithType(entries)
-	sessionTypes := section.BuildTypeIndex(typeEntries)
-
-	// Build topic lookup for related footer
-	topicIndex := moc.BuildTopicLookup(topicEntries)
-
-	// Transform and write entries
-	for _, entry := range entries {
-		src := entry.Path
-		dst := filepath.Join(output, obsidian.DirEntries, entry.Filename)
-
-		content, readErr := io.SafeReadUserFile(filepath.Clean(src))
-		if readErr != nil {
-			err.WarnFile(cmd, entry.Filename, readErr)
-			continue
-		}
-
-		// Normalize content (read-only - do NOT write back to source)
-		normalized := wrap.Content(
-			turn.MergeConsecutive(
-				consolidate.ToolRuns(
-					reduce.CleanToolOutputJSON(
-						reduce.StripSystemReminders(string(content)),
-					),
-				),
-			),
-		)
-
-		// Transform for Obsidian
-		sourcePath := filepath.Join(
-			dir.Context, dir.Journal, entry.Filename,
-		)
-		transformed := frontmatter.Transform(normalized, sourcePath)
-		transformed = wikilink.ConvertMarkdownLinks(transformed)
-		transformed += moc.GenerateRelatedFooter(
-			entry, topicIndex, obsidian.MaxRelated,
-		)
-
-		if writeErr := io.SafeWriteFile(
-			dst, []byte(transformed), fs.PermFile,
-		); writeErr != nil {
-			err.WarnFile(cmd, entry.Filename, writeErr)
-			continue
-		}
-	}
-
-	// Write topic MOC and pages
-	if len(topics) > 0 {
-		topicsDir := filepath.Join(output, dir.JournTopics)
-		mocPath := filepath.Join(output, obsidian.MOCTopics)
-		if writeErr := io.SafeWriteFile(
-			mocPath, []byte(moc.ObsidianTopics(topics)),
-			fs.PermFile,
-		); writeErr != nil {
-			return errFs.FileWrite(mocPath, writeErr)
-		}
-
-		for _, t := range topics {
-			if !t.Popular {
-				continue
-			}
-			pagePath := filepath.Join(topicsDir, t.Name+file.ExtMarkdown)
-			if writeErr := io.SafeWriteFile(
-				pagePath, []byte(moc.GenerateObsidianTopicPage(t)),
-				fs.PermFile,
-			); writeErr != nil {
-				err.WarnFile(cmd, pagePath, writeErr)
-			}
-		}
-	}
-
-	// Write key files MOC and pages
-	if len(keyFiles) > 0 {
-		filesDir := filepath.Join(output, dir.JournalFiles)
-		mocPath := filepath.Join(output, obsidian.MOCFiles)
-		if writeErr := io.SafeWriteFile(
-			mocPath, []byte(moc.ObsidianFiles(keyFiles)),
-			fs.PermFile,
-		); writeErr != nil {
-			return errFs.FileWrite(mocPath, writeErr)
-		}
-
-		for _, kf := range keyFiles {
-			if !kf.Popular {
-				continue
-			}
-			slug := format.KeyFileSlug(kf.Path)
-			pagePath := filepath.Join(filesDir, slug+file.ExtMarkdown)
-			if writeErr := io.SafeWriteFile(
-				pagePath, []byte(moc.GenerateObsidianFilePage(kf)),
-				fs.PermFile,
-			); writeErr != nil {
-				err.WarnFile(cmd, pagePath, writeErr)
-			}
-		}
-	}
-
-	// Write types MOC and pages
-	if len(sessionTypes) > 0 {
-		typesDir := filepath.Join(output, dir.JournalTypes)
-		mocPath := filepath.Join(output, obsidian.MOCTypes)
-		if writeErr := io.SafeWriteFile(
-			mocPath, []byte(moc.ObsidianTypes(sessionTypes)),
-			fs.PermFile,
-		); writeErr != nil {
-			return errFs.FileWrite(mocPath, writeErr)
-		}
-
-		for _, st := range sessionTypes {
-			pagePath := filepath.Join(typesDir, st.Name+file.ExtMarkdown)
-			if writeErr := io.SafeWriteFile(
-				pagePath,
-				[]byte(moc.GenerateObsidianTypePage(st)), fs.PermFile,
-			); writeErr != nil {
-				err.WarnFile(cmd, pagePath, writeErr)
-			}
-		}
-	}
-
-	// Write Home.md
-	homePath := filepath.Join(output, obsidian.MOCHome)
-	if writeErr := io.SafeWriteFile(
-		homePath,
-		[]byte(moc.Home(
-			regularEntries,
-			len(topics) > 0, len(keyFiles) > 0, len(sessionTypes) > 0,
-		)),
-		fs.PermFile,
-	); writeErr != nil {
-		return errFs.FileWrite(homePath, writeErr)
-	}
-
-	writeObsidian.InfoGenerated(cmd, len(entries), output)
-
-	return nil
-}