pensar 0.6.3

Bug fixes

• vault_graph()’s control-file filter now works on Windows. The previous implementation compared dirname(file) against normalizePath(vault), but dirname() on Windows uses forward slashes in its output while normalizePath() defaults to backslashes, so the comparison was always false on Windows. Control files (schema.md, index.md, log.md) leaked into the graph, and the “No pages in vault” guard never fired on an empty vault. Now normalises vault with winslash = "/" so the comparison matches dirname()’s output on both platforms.
• inst/tinytest/test_vault_graph.R’s empty-vault regression test is now between the saber-installed and saber-graph_svg guards so it runs on machines whose saber is still at the current CRAN release (0.3.0). Without this, the win-builder farm was the only place exercising the bug.

pensar 0.6.2

Bug fixes

• vault_graph() no longer crashes on Windows. category_from_path() built a regex from the vault path; on Windows the backslashes were interpreted as regex backreferences, halting R CMD check on the CRAN win-builder farm with “Invalid back reference”. The helper now strips the vault prefix by substring and handles both / and \ separators.
• inst/tinytest/test_vault_graph.R had a top-of-file exit_file("installed saber lacks graph_svg(); skipping") that skipped the entire file when saber was at the current CRAN release (0.3.0). The category_from_path() regression tests are now above that guard so they run regardless of which saber is installed.

pensar 0.6.1

New features

• autoresearch(topic, vault, ...) runs a bounded, package-owned research workflow into a pensar vault. R controls the loop, source ingestion, wiki writes, indexing, and logging; model calls are limited to structured decisions returned as JSON (plan_queries, select_sources, extract_claims, analyze_gaps, plan_pages, revise_page). Multi-round gap analysis driven by program$max_rounds. Prompt-injection guards flag fetched source bodies. update = TRUE (default) preserves user prose on re-runs via a revise_page model task; the heuristic fallback appends new findings under a dated section so prose is never lost. Default search backend uses Tavily via TAVILY_API_KEY; default model backend uses llm.api when any of ANTHROPIC_API_KEY, OPENAI_API_KEY, or MOONSHOT_API_KEY is set, with a deterministic heuristic backend so the full pipeline runs without LLM access.
• init_vault(path, adopt = TRUE) adoption is now verified against six real Obsidian vaults via inst/tinytest/test_adopt_real.R (gated by tinytest::at_home() and the PENSAR_TEST_VAULTS env var). The mechanism was already covered by test_adopt.R against synthetic directories; the new test adds real-world coverage for bramses-highly-opinionated-vault-2023, claude-obsidian, dusk-obsidian-vault, kepano-obsidian, Obsidian-Vault-Structure, and obsidian-wiki.
• New vignette adopt-obsidian.md documents adopt-mode semantics and walks through the six-vault sweep.

Internals

• ingest_url() is now layered on fetch_url_content() and ingest_url_content() (both internal), so the autoresearch loop can fetch once and keep the body in memory for evidence extraction.
• write_wiki_page() (internal) merges frontmatter on update instead of clobbering: existing id, aliases, status, related, and any custom keys survive an update; tags are set-unioned; caller-supplied fields replace existing values; body is always replaced. Refuses writes into adopted vaults unless force = TRUE. Refuses to overwrite an existing wiki file when overwrite = FALSE.
• autoresearch() calls vault_commit() after writes, matching ingest()’s pattern, so git-backed vaults stay clean.
• extract_html_title() handles multi-line HTML titles via PCRE.

Skill bundle

• inst/skills/pensar/autoresearch/SKILL.md rewritten to route research requests through autoresearch() rather than reproducing a manual WebSearch/WebFetch/file-edit loop. The runtime program ships as machine-readable YAML at inst/autoresearch/program.yml, overridable by <vault>/_research/program.yml. Architecture note at inst/autoresearch/architecture.md.

DESCRIPTION

• Recentered prose around personal wiki + LLM research assistant + manual editing. Mentions autoresearch(), the 'Claude Code' skill bundle, the seeded 'CLAUDE.md' / 'AGENTS.md' files for 'Codex' compatibility, and adopt mode for existing 'Obsidian' vaults.
• New Suggests: jsonlite, llm.api, simplermarkdown. Vignette builder: simplermarkdown.

pensar 0.6.0.1

• ingest_agent_context() now resolves saber::agent_context() dynamically via getExportedValue() instead of a static reference. Older saber versions (pre-0.4, including CRAN’s current 0.3.0) that don’t export agent_context() get a clean error message instead of tripping R CMD check’s “Missing or unexported object” static analysis and failing the test suite. Test gates symmetrically so it exercises either the success path or the missing-export path depending on which saber is installed.
• test_vault_graph test similarly gates on "graph_svg" %in% getNamespaceExports("saber") so the suite passes cleanly against CRAN saber 0.3.0 (which lacks graph_svg). vault_graph() itself already gated its saber::graph_svg() call; only the test needed the matching guard.

pensar 0.6.0

A foundation release that fixes a destructive bug in init_vault(), introduces an adopt mode for existing Obsidian vaults, adds a registry-based identity layer, ships per-source manifest bookkeeping, exposes retrieval primitives, brings in URL ingest, dedup / tag audits, an agent-context snapshot wrapper, and a markdown skill bundle for autonomous web research.

Safety

• init_vault() refuses to scaffold into directories that already contain non-pensar files or a foreign git history. Pass adopt = TRUE for read-only adoption (below) or force = TRUE to scaffold anyway. The auto-commit step is gated separately via a new commit parameter (default NULL): commits only when the directory was pensar-owned before scaffolding, never as a side effect of force = TRUE. Fixes a destructive default where pointing init_vault() at someone else’s git repo would write scaffolding and an auto-commit into their history.
• The ownership heuristic requires schema.md as the load-bearing marker. Top-level raw/ or wiki/ directories without schema.md are treated as foreign.

Foundation

• New vault_registry(vault, cache, refresh) builds a data.frame with one row per page: path, node_id (current link-resolution identity), page_uid (stable identity from frontmatter id: / address:; NA otherwise), title, aliases, type, category, tags, sources, links_out, system_file. Caches in a session env by default; cache = "user" persists to tools::R_user_dir("pensar", "cache"). Never writes inside the vault. Cache invalidates on rename via per-file path+mtime+size signature.
• find_page() and all its consumers (outlinks(), backlinks(), lint()) resolve through the registry: exact path → page_uid → unique node_id → ambiguous-basename warning → frontmatter alias. Path-style wikilinks ([[Notes/Foo]]), .md-suffix links, and #section / #^block-id anchors all resolve correctly. System files (schema.md, index.md, log.md, _proposals/*) are skipped in fuzzy resolution so user pages always win shadow conflicts.
• New init_vault(adopt = TRUE) for opt-in read-only adoption of existing Obsidian vaults. Writes only a minimal adopted schema.md (adopted: true frontmatter), log.md, and index.md if missing. No raw//wiki/ scaffolding, no auto-commit, leaves user content untouched. Pre-existing log.md is preserved. update_index() and status() switch to registry-driven enumeration for adopted vaults, grouping by frontmatter type (falling back to category). ingest() refuses to write into adopted vaults unless force = TRUE. Path-disambiguated index links ([[A/Foo]] / [[B/Foo]]) when basenames collide.
• New manifest_path(), read_manifest(), update_manifest(). Per-source ingest provenance plus an opt-in address_map. Lives at .pensar/manifest.yml. ingest() and ingest_repo() hook into the manifest after successful writes with a sha1: content hash. Read-only ops never touch it. Malformed sub-fields and per-entry records degrade safely instead of crashing.
• Read-side compatibility with .manifest.json and .raw/.manifest.json is deferred; would require jsonlite in Imports.

New features

• Retrieval primitives (registry-backed, write-free):
  • search_pages(query, vault, type, in_body) substring-matches over title / tags / aliases by default; in_body = TRUE also scans page bodies. Returns a matched_in column. Excludes system control files.
  • page_context(name, vault, body_chars) returns a structured view of one page: frontmatter, body_head, outlinks, backlinks.
  • related_pages(name, vault, k) ranks top-k by shared tags + shared outlinks (canonical-path co-citation).
  • recent_activity(vault, days) parses log.md, newest first.
• New ingest_url(url, vault, type, title, tags) fetches via curl::curl_fetch_memory() (10s timeout, follow-redirects, TLS verify on). Refuses non-2xx and content types outside text/html, text/plain, text/markdown, application/json, application/xml, text/xml. HTML responses use <title> as the page title when none is supplied. Dedup against the manifest: same URL twice doesn’t re-fetch. Skips and re-fetches when the recorded file has been deleted or the entry is malformed.
• New dedup(vault, threshold) proposes candidate duplicate pages by combining Jaro-Winkler title similarity (60%) and tag-set Jaccard overlap (40%). Writes to _proposals/dedup.md. Never auto-merges.
• New tags(vault, taxonomy) audits used tags against an optional controlled vocabulary at _meta/taxonomy.md (markdown bullet list). Unknown tags get near-miss suggestions via Jaro-Winkler. Writes to _proposals/tags.md. Never auto-renames. Explicit missing taxonomy path errors instead of silently degrading.
• New ingest_agent_context(agent, vault, ...) wraps saber::agent_context() to snapshot the live agent context (memory, project / global instructions, identity files) into the vault as a raw/chats/ page. Saber stays in Suggests; missing saber errors with an install hint.

Skills

• Pensar ships an agent skill bundle at inst/skills/pensar/autoresearch/: SKILL.md driving a bounded 3-round web-research loop (decompose → search/fetch → gap fill → synthesize) and a configurable references/program.md. The loop files results through ingest_url(), dedups concepts with search_pages(), suggests cross-links via related_pages(), and refreshes the index plus log on completion.
• New pensar_skill_path(skill = NULL) returns the absolute path to the bundle root or a specific skill. Symlink it into an agent’s skill directory: ln -s $(Rscript -e 'cat(pensar::pensar_skill_path())') \ ~/.claude/skills/pensar.

Internals

• Read-only operations (vault_registry(), update_index(), status(), backlinks(), outlinks(), lint(), search_pages(), page_context(), related_pages(), recent_activity()) never write vault state. .pensar/ is reserved for vault-owned bookkeeping; derived caches live in tools::R_user_dir("pensar", "cache").
• lint() now reads tag and link data from the registry instead of re-parsing files, and keys tag-cluster raw pages by relative path so duplicate basenames in different folders no longer collide and undercount clusters.
• outlinks() surfaces ambiguous-target warnings to interactive callers; backlinks() and lint() continue to use a muffling resolver helper since they iterate.
• Walk-up vault discovery also checks <dir>/vault/schema.md at each rung, so running pensar from a project root whose vault lives one level down (e.g., cornelius/vault/) resolves correctly.
• status() records the resolver source on the returned pensar_status object ($source is one of "env", "walkup", "walkup-subdir", "option", "explicit") and surfaces it in the print method.

Dependencies

• New Imports: curl (URL ingest), digest (registry cache key
  • content hashes), stringdist (Jaro-Winkler for dedup and near-miss tags). saber remains in Suggests.

pensar 0.5.0

• New ingest_repo(path) writes per-repo provenance under raw/repos/<repo>/: briefing.md (saber digest), ast.md (saber::symbols() output), and snapshot.md (commit-pinned metadata: SHA, origin URL, branch, tracked file listing). Wiki pages cite them with path-style wikilinks like [[corteza/briefing]].
• name_from_path() is now path-aware: files under raw/repos/<repo>/ resolve to <repo>/<basename>, so artifacts named briefing.md across different repos do not collide. Files outside raw/repos/ are unchanged.
• update_index() reports a new Raw: Repos category.
• ingest_briefing() is deprecated; calls now warn and delegate to ingest_repo(path, artifacts = "briefing").
• New migrate_briefings_to_repos(vault, dry_run = TRUE) moves legacy raw/briefings/*.md content into raw/repos/<repo>/. Keeps the newest file per (repo, artifact) pair, drops superseded duplicates by default, rewrites wikilinks across wiki/*.md. The built-in rename map handles llamaR -> corteza; pass an extended map for other renames. Defaults to dry-run; review the plan first.
• Schema doc updated to describe the raw/repos/<repo>/<artifact> layout and mark briefings/ deprecated.

pensar 0.4.3

• vault_export() returns a canonicalized out_dir so the path is stable across calls. On macOS tempdir() lives under /var/... which is a symlink to /private/var/...; normalizePath() only resolves symlinks for paths that exist, so the first call returned the unresolved form and the second returned the resolved form, breaking idempotency. Re-normalizing after dir.create() fixes the M1mac CRAN check failure.

pensar 0.4.2

• CRAN review compliance.
• default_vault() and default_site_dir() no longer fall back to tools::R_user_dir(). Per CRAN policy pensar will not silently write to the user’s home filespace; if no vault is configured via PENSAR_VAULT, walk-up schema.md, or options("pensar.vault"), the call errors with a setup hint. Pass vault = (or path = for init_vault()) explicitly to write to a one-off path. Breaking for users who relied on the implicit ~/.local/share/R/pensar/ fallback – run use_vault('/path/to/vault') once or set PENSAR_VAULT to restore the previous behavior.
• vault_export() now requires either PENSAR_SITE_DIR or an explicit out_dir =; the cache fallback is gone for the same reason.
• Title shortened to LLM Wiki Engine. Description tidied. Added SystemRequirements: pandoc, git. Dropped unused jsonlite from Suggests.
• Every exported function now has a runnable @examples block, using tempdir() / tempfile() so nothing leaks into the user’s home filespace at example time.
• vault_graph() and ingest_briefing() error messages reworded to drop the GitHub install URL.

pensar 0.4.1

• default_vault() resolution order changed so project-local vaults beat a global .Rprofile default. New order: PENSAR_VAULT env var > walk-up from getwd() for a schema.md marker > the options("pensar.vault") value set by use_vault() > the R_user_dir() fallback. Previously the option won over the env var, which made PENSAR_VAULT=... ineffective once use_vault() ran in .Rprofile. Walk-up is new: cd into a project vault and the CLI Just Works without unsetting your global default.

pensar 0.4.0

• New vault_graph() renders the vault’s wikilink graph as static SVG via saber::graph_svg(). Tooltips carry title, type, date, tags, and a lede from the first meaningful body line. Broken wikilinks appear as separate nodes. Default viewport 1600x1200 for denser vaults.

pensar 0.3.1

• default_vault() now honors options("pensar.vault") and the PENSAR_VAULT environment variable before falling back to tools::R_user_dir("pensar", "data"). Previously, the vault path was hardcoded to the R_user_dir() path with no escape hatch, so a nicer path like ~/wiki required passing vault = to every call.
• New use_vault() sets options("pensar.vault") for the session, mirroring hacer::use_repo().

pensar 0.3.0

• New ingest_briefing() generates a saber briefing via saber::briefing() and ingests it into the vault. Replaces the direct cache-file read in inst/scripts/session-start.R with a real function call, so briefings refresh on ingest instead of depending on saber’s hook having run first.
• saber added to Suggests (previously coupled only via filesystem).

pensar 0.2.0

• Initial release: LLM wiki engine with init_vault(), ingest(), update_index(), log_entry(), status(), backlinks(), outlinks(), show_page(), lint(), and vault_export().