16 changed files with 988 additions and 2700 deletions
--- a/CLAUDE.md
+++ b/CLAUDE.md
@ -10,21 +10,18 @@
 ## Current Project State
- **Phase:** Active development — Phases 1, 2, 2.5, 2.6, 2.7, 2.8, 3 complete. Next: fix #78 (synthesis persistence), #79 (stale cache), then reassess Phase 4+ (#40).
+- **Phase:** Active development — Phase 2 (survey pass) and Phase 2.5 (context budget) complete; Phase 3 (investigation planning) ready to start
- **Last worked on:** 2026-04-12
+- **Last worked on:** 2026-04-06
- **Last commit:** fix(ai): match target root by basename in _apply_plan() (#76)
+- **Last commit:** merge: feat/issue-44-context-budget (#44)
 - **Blocking:** None
 - **Test count:** 262 passing
 ---
 ## Project Overview
-Luminos is a file system intelligence tool. Point it at a directory and it
+Luminos is a file system intelligence tool — a zero-dependency Python CLI that
-runs a multi-pass agentic investigation via the Claude API: a survey pass,
+scans a directory and produces a reconnaissance report. With `--ai` it runs a
-isolated dir-loop agents per directory, and a synthesis pass that produces a
+multi-pass agentic investigation via the Claude API.
 project-level verdict with severity-ranked flags. A lightweight base scan
 runs first to feed the agent its initial picture of the target.
 ---
@ -35,7 +32,8 @@ runs first to feed the agent its initial picture of the target.
 | `luminos.py` | Entry point — arg parsing, scan(), main() |
 | `luminos_lib/ai.py` | Multi-pass agentic analysis via Claude API |
 | `luminos_lib/ast_parser.py` | tree-sitter code structure parsing |
-| `luminos_lib/cache.py` | Investigation cache management (incl. clear_cache) |
+| `luminos_lib/cache.py` | Investigation cache management |
 | `luminos_lib/capabilities.py` | Optional dep detection, cache cleanup |
 | `luminos_lib/code.py` | Language detection, LOC counting |
 | `luminos_lib/disk.py` | Per-directory disk usage |
 | `luminos_lib/filetypes.py` | File classification (7 categories) |
@ -43,6 +41,7 @@ runs first to feed the agent its initial picture of the target.
 | `luminos_lib/recency.py` | Recently modified files |
 | `luminos_lib/report.py` | Terminal report formatter |
 | `luminos_lib/tree.py` | Directory tree visualization |
 | `luminos_lib/watch.py` | Watch mode with snapshot diffing |
 Details: wiki — [Architecture](https://forgejo.labbity.unbiasedgeek.com/archeious/luminos/wiki/Architecture) | [Development Guide](https://forgejo.labbity.unbiasedgeek.com/archeious/luminos/wiki/DevelopmentGuide)
@ -50,52 +49,72 @@ Details: wiki — [Architecture](https://forgejo.labbity.unbiasedgeek.com/archei
 ## Key Constraints
- **AI investigation is the product.** The base scan exists to feed the agent.
+- **Base tool: no pip dependencies.** tree, filetypes, code, disk, recency,
-  There is no `--ai` flag and no `--no-ai` mode. AI runs unconditionally on
+  report, watch use only stdlib and GNU coreutils. Must always work on bare Python 3.
-  every invocation.
+- **AI deps are lazy.** `anthropic`, `tree-sitter`, `python-magic` imported only
- **Anthropic API key is required.** If `ANTHROPIC_API_KEY` is unset, luminos
+  when `--ai` is used. Missing packages produce a clear install error.
  exits cleanly (exit 0) with a one-line hint instead of running.
 - **Dependencies installed via `requirements.txt`.** anthropic, tree-sitter +
  grammars, and python-magic are normal pip dependencies, not lazy imports.
  `setup_env.sh` creates a venv and installs them.
 - **Subprocess for OS tools.** LOC counting, file detection, disk usage, and
  recency shell out to GNU coreutils. Do not reimplement in pure Python.
 - **Graceful degradation everywhere.** Permission denied, subprocess timeouts,
-  individual dir-loop failures — all handled without crashing the run.
+  missing API key — all handled without crashing.
 ---
 ## Running Luminos
 ```bash
-# Activate the venv (one-time setup: ./setup_env.sh)
+# Base scan
 source ~/luminos-env/bin/activate
 export ANTHROPIC_API_KEY=your-key-here
 # Run an investigation
 python3 luminos.py <target>
 # With AI analysis (requires ANTHROPIC_API_KEY)
 source ~/luminos-env/bin/activate
 python3 luminos.py --ai <target>
 # Common flags
 python3 luminos.py -d 8 -a -x .git -x node_modules <target>
 python3 luminos.py --json -o report.json <target>
-python3 luminos.py --fresh <target>
+python3 luminos.py --watch <target>
-python3 luminos.py --clear-cache
+python3 luminos.py --install-extras
 ```
 ---
-## Project-Specific Test Notes
+## Development Workflow
-Run tests with `python3 -m unittest discover -s tests/`. Modules exempt from
+- **Issue-driven work** — all work must be tied to a Forgejo issue. If the
-unit testing: `ast_parser.py` (requires tree-sitter grammars at import time)
+  user names a specific issue, use it. If they describe work without an issue
-and `prompts.py` (string templates only). `ai.py` is partially covered:
+  number, search open issues for a match. If no issue exists, gather enough
-end-to-end loops require a live Anthropic API and stay exempt, but the pure
+  context to create one before starting work. Branches and commits should
-helpers (`_filter_dir_tools`, `_format_survey_block`, `_path_is_safe`,
+  reference the issue number.
-`_should_skip_dir`, `_block_to_dict`, `_flush_partial_dir_entry`, etc.) are
+- **Explain then build** — articulate the approach in a few bullets before
-covered by `tests/test_ai_pure.py`.
+  writing code. Surface assumptions early.
 - **Atomic commits** — each commit is one logical change.
 - **Test coverage required** — every change to a testable module must include
  or update tests in `tests/`. Run with `python3 -m unittest discover -s tests/`.
  All tests must pass before merging. Modules exempt from unit testing:
  `ai.py` (requires live API), `ast_parser.py` (requires tree-sitter),
  `watch.py` (stateful events), `prompts.py` (string templates only).
 - **Shiny object capture** — new ideas go to PLAN.md (Raw Thoughts) or a
  Forgejo issue, not into current work.
-(Development workflow, branching discipline, and session protocols live in
+---
-`~/.claude/CLAUDE.md`.)
+
 ## Branching Discipline
 - **Always branch** — no direct commits to main, ever
 - **Branch before first change** — create the branch before touching any files
 - **Naming:** `feat/`, `fix/`, `refactor/`, `chore/` + short description
 - **One branch, one concern** — don't mix unrelated changes
 - **Two-branch maximum** — never have more than 2 unmerged branches
 - **Merge with `--no-ff`** — preserves branch history in the log
 - **Delete after merge** — `git branch -d <branch>` immediately after merge
 - **Close the underlying issue manually** — after merging, `PATCH` the
  referenced issue to `state: closed` via the Forgejo API. Do not rely
  on `Closes #N` keyword auto-close — it has not worked reliably in
  this Forgejo instance, leaving issues stale while their PRs are
  merged. Manual close is one extra API call and is part of the merge
  step, not optional.
 - **Push after commits** — keep Forgejo in sync after each commit or logical batch
 ---
@ -107,17 +126,71 @@ covered by `tests/test_ai_pure.py`.
 | Classes | PascalCase | `_TokenTracker`, `_CacheManager` |
 | Constants | UPPER_SNAKE_CASE | `MAX_CONTEXT`, `CACHE_ROOT` |
 | Module files | snake_case | `ast_parser.py` |
-| CLI flags | kebab-case | `--clear-cache`, `--fresh` |
+| CLI flags | kebab-case | `--clear-cache`, `--install-extras` |
 | Private functions | leading underscore | `_run_synthesis` |
 ---
 ## Documentation Workflow
 - **Wiki location:** `docs/wiki/` — local git checkout of `luminos.wiki.git`
 - **Clone URL:** `ssh://git@forgejo-claude/archeious/luminos.wiki.git`
 - **Session startup:** clone if missing, `git -C docs/wiki pull` if present
 - **All reads and writes** happen on local files in `docs/wiki/`. Use Read,
  Edit, Write, Grep, Glob — never the Forgejo web API for wiki content.
 - **Naming:** CamelCase slugs (`Architecture.md`, `DevelopmentGuide.md`).
  Display name comes from the H1 heading inside the file.
 - **Commits:** direct to main branch. Batch logically — commit when finishing
  a round of updates, not after every file.
 - **Push:** after each commit batch.
 ---
 ## ADHD Session Protocols
 > **MANDATORY — follow literally, every session, no exceptions.**
 1. **Session Start Ritual** — Ensure `docs/wiki/` is cloned and current.
   Fetch open issues from Forgejo (`archeious/luminos`) and present them as
   suggested tasks. Ask: *"What's the one thing we're shipping?"* Once the
   user answers, match to an existing issue or create one before starting
   work. Do NOT summarize project state, recap history, or do any other work
   before asking this question.
 2. **Dopamine-Friendly Task Sizing** — break work into 5–15 minute tasks with
   clear, visible outputs. Each task should have a moment of completion.
 3. **Focus Guard** — classify incoming requests as on-topic / adjacent /
   off-topic. Name it out loud before acting. Adjacent work goes to a new
   issue; off-topic work gets deferred.
 4. **Shiny Object Capture** — when a new idea surfaces mid-session, write it
   to PLAN.md (Raw Thoughts) or open a Forgejo issue, then return to the
   current task. Do not context-switch.
 5. **Breadcrumb Protocol** — after each completed task, output:
   `Done: <what was completed>. Next: <what comes next>.`
   This re-orients after any interruption.
 6. **Session End Protocol** — before closing, state the exact pickup point for
   the next session: branch name, file, what was in progress, and the
   recommended first action next time.
 ---
 ## Session Protocols
 - **"externalize"** → read and follow `docs/externalize.md`
 - **"wrap up" / "end session"** → read and follow `docs/wrap-up.md`
 ---
 ## Session Log
 | # | Date | Summary |
 |---|---|---|
-| 8 | 2026-04-07 | Closed #54 — added confidence/confidence_reason to write_cache tool schema description; Phase 1 milestone now 4/4 complete |
+| 2 | 2026-04-06 | Forgejo milestones (9), issues (36), project board, Gitea MCP installed and configured globally |
-| 9 | 2026-04-11 | Scope shift (#64) + ALL Phase 3 prereqs: dir loop refactor (#57), tool registry consolidation (#56), pure-helper test coverage waves 1+2 (#55, #70), leaf-first contract docs (#72). 6 PRs, 70 net new tests (164→234), Phase 2.6/2.7/2.8 milestones complete |
+| 3 | 2026-04-06 | Phase 1 complete (#1–#3), MCP backend architecture design (Part 10, Phase 3.5), issues #38–#40 opened |
-| 10 | 2026-04-12 | Phase 3 shipped: planning pass, dynamic turn allocation, quality instrumentation (#8, #9, #10, #11, #74). Fixed root-path matching bug (#76). Smoke tests on luminos + homelab IaC. Filed #78 (synthesis persistence), #79 (stale cache). 3 PRs, 28 new tests (234→262) |
+| 4 | 2026-04-06 | Phase 2 + 2.5 complete (#4–#7, #42, #44), filetype classifier rebuild, context budget metric fix, 8 PRs merged, issues #46/#48/#49/#51 opened |
 Full log: wiki — [Session Retrospectives](https://forgejo.labbity.unbiasedgeek.com/archeious/luminos/wiki/SessionRetrospectives)
--- a/202
+++ b/202
@ -1,202 +0,0 @@
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--- a/PLAN.md
+++ b/PLAN.md
@ -576,46 +576,6 @@ without 9 phases of rework.
  output size, redundant reads) before picking a fix.
 - Add token-usage instrumentation so regressions are visible.
 ### Phase 2.6 — Pre-Phase-3 cleanup (#54, #57) ✅ shipped
 Two debts surfaced during the Session 5 documentation deep dive that
 were paid before Phase 3 adds more state to the same code paths:
 - **#54** — Phase 1 confidence-write path was dormant. Cache schema
  accepted `confidence` and `low_confidence_entries()` worked, but no
  prompt instructed the agent to set the field. Wired in Session 8.
 - **#57** — `_run_dir_loop` was ~160 lines holding four conceptual
  layers. Refactored in Session 9 into three focused helpers
  (`_build_dir_loop_context`, `_flush_partial_dir_entry`,
  `_handle_turn_response`) so Phase 3 dynamic turn allocation has a
  thin coordinator to inject into.
 ### Phase 2.7 — Tool registration cleanup (#56) ✅ shipped
 Adding a tool used to require updating `_TOOL_DISPATCH` and `_DIR_TOOLS`
 in two separate places. Forgetting one half was silent. Replaced both
 with a single `register_tool()` call per (tool, scope) in Session 9.
 Phase 3.5 MCP backend will eventually replace this with dynamic
 discovery, at which point `register_tool()` collapses to a one-line
 forward.
 ### Phase 2.8 — Pre-Phase-3 test coverage (#55, #70)
 Safety nets for the helpers Phase 3 will pile state on top of. Two
 waves:
 - **#55** ✅ shipped — `tests/test_ai_pure.py` covers the easy
  decision-logic helpers: `_filter_dir_tools`, `_format_survey_block`,
  `_format_survey_signals`, `_default_survey`, `_should_skip_dir`,
  `_path_is_safe`, `_block_to_dict`, plus `_flush_partial_dir_entry`
  from #57. 45 tests added in Session 9.
 - **#70** — second wave covering the highest-impact remaining helpers
  that escaped the first sweep:
  - `_TokenTracker` — pins the load-bearing #44 fix
    (`last_input` vs cumulative for budget decisions)
  - `_synthesize_from_cache` — last-resort fallback that fires almost
    never in normal runs and is therefore the kind of code that silently
    rots
  - `_discover_directories` — leaves-first walk and skip-dir filter,
    foundation of the cache reuse story
 ### Phase 3 — Investigation planning
 - Planning pass after survey, before dir loops
 - `submit_plan` tool
@ -692,7 +652,7 @@ architecture. The migration pain is intentional and instructive.
  extension sub-section or similar. Low priority, not blocking.
 - **Revisit survey-skip thresholds (#46)** — `_SURVEY_MIN_FILES` and
  `_SURVEY_MIN_DIRS` shipped with values from #7's example, no
-  empirical basis. Once luminos has been run on a variety of real
+  empirical basis. Once `--ai` has been run on a variety of real
  targets, look at which runs skipped the survey vs ran it and decide
  whether the thresholds (or the gate logic itself) need to change.
@ -711,7 +671,7 @@ architecture. The migration pain is intentional and instructive.
 | `luminos_lib/search.py` | **new** — web_search, fetch_url, package_lookup implementations |
 No changes needed to: `tree.py`, `filetypes.py`, `code.py`, `recency.py`,
-`disk.py`, `ast_parser.py`
+`disk.py`, `capabilities.py`, `watch.py`, `ast_parser.py`
 ---
@ -803,20 +763,20 @@ agent read, in what order, what it decided to skip). Storing the full message
 history per directory would allow replaying or auditing an investigation. Cost:
 storage. Benefit: debuggability, ability to resume investigations more faithfully.
-**Live re-investigation mode**
+**Watch mode + incremental investigation**
-A "watch" replacement: detect which directories changed, re-investigate only
+Watch mode currently re-runs the full base scan on changes. For AI-augmented
-those, and patch the cache entries. The synthesis would then re-run from the
+watch mode: detect which directories changed, re-investigate only those, and
-updated cache without re-investigating unchanged directories. The original
+patch the cache entries. The synthesis would then re-run from the updated cache
-non-AI watch mode was deleted in the #64 scope change because it conflicted
+without re-investigating unchanged directories.
 with the AI-first philosophy. If watch comes back, it comes back as this.
-**PDF and Office document readers**
+**Optional PDF and Office document readers**
 The data and documents domains would benefit from native content extraction:
 - `pdfminer` or `pypdf` for PDF text extraction
 - `openpyxl` for Excel schema and sheet enumeration
 - `python-docx` for Word document text
-These slot into `requirements.txt` like any other dependency. The agent
+These would be optional deps like the existing AI deps, gated behind
-currently can only see filename and size for these formats.
+`--install-extras`. The agent currently can only see filename and size for
 these formats.
 **Security-focused analysis mode**
 A `--security` flag could tune the investigation toward security-relevant
@ -879,6 +839,11 @@ bad plan wastes turns on shallow directories and skips critical ones. The system
 needs quality signals — probably the confidence scores aggregated across the
 investigation — to detect when something went wrong and potentially retry.
 **Watch mode compatibility**
 Several of the planned features (survey pass, planning, external tools) are not
 designed for incremental re-use in watch mode. Adding AI capability to watch
 mode is a separate design problem that deserves its own thinking.
 **Turn budget contention**
 If the planning pass allocates turns and the agent borrows from its budget when
 it needs more, there's a risk of runaway investigation on unexpectedly complex
--- a/README.md
+++ b/README.md
@ -1,103 +0,0 @@
 # Luminos
 A file system intelligence tool. Point it at a directory and it runs an agentic Claude investigation that figures out what the directory is, what's in it, and what might be worth your attention.
 Luminos is built around a harder question than "what files are here?" It is built around "what is this, and should I be worried about any of it?" To answer that, it runs a multi-pass agentic investigation against the [Claude API](https://www.anthropic.com/api): a survey pass to orient on the target, an isolated dir-loop agent per directory with a small toolbelt (read files, run whitelisted coreutils commands, write cache entries), and a final synthesis pass that produces a project-level verdict with severity-ranked flags.
 A lightweight base scan runs first to feed the agent its initial picture of the target. The base scan is not a standalone product, it is the first step of the investigation.
 ## Features
 - **Agentic AI investigation.** Multi-pass, leaves-first analysis via Claude. Survey then dir loops then synthesis.
 - **Investigation cache.** Per-file and per-directory summaries are cached under `/tmp/luminos/` so repeat runs on the same target are cheap.
 - **Severity-ranked flags.** Findings are sorted so `critical` items are the first thing you see.
 - **Context budget guard.** Per-turn `input_tokens` is watched against a budget so a rogue directory can't blow the context and silently degrade quality.
 - **Graceful degradation.** Permission denied, subprocess timeouts, missing API key: all handled without crashing.
 - **JSON output.** Pipe reports to other tools or save for comparison.
 ## Installation
 Luminos is a normal Python project. Clone, create a venv, and install from `requirements.txt`. The repository ships a helper script that does this for you:
 ```bash
 git clone https://github.com/archeious/luminos.git
 cd luminos
 ./setup_env.sh
 source ~/luminos-env/bin/activate
 ```
 Or do it by hand:
 ```bash
 python3 -m venv ~/luminos-env
 source ~/luminos-env/bin/activate
 pip install -r requirements.txt
 ```
 You also need an Anthropic API key exported as an environment variable:
 ```bash
 export ANTHROPIC_API_KEY=your-key-here
 ```
 The base scan shells out to a handful of GNU coreutils (`wc`, `file`, `grep`, `head`, `tail`, `stat`, `du`, `find`), so you also need those on `$PATH`. They are installed by default on every mainstream Linux distribution and on macOS via Homebrew.
 ## Usage
 ```bash
 python3 luminos.py /path/to/project
 ```
 That is the whole interface. The investigation runs end to end and prints a report.
 ### Common flags
 ```bash
 # Deeper tree, include hidden files, exclude build and vendor dirs
 python3 luminos.py -d 8 -a -x .git -x node_modules -x vendor /path/to/project
 # JSON output to a file
 python3 luminos.py --json -o report.json /path/to/project
 # Force a fresh investigation, ignoring the cache
 python3 luminos.py --fresh /path/to/project
 # Clear the investigation cache
 python3 luminos.py --clear-cache
 ```
 Run `python3 luminos.py --help` for the full flag list.
 ## How the investigation works
 A short version of what happens on every run:
 1. **Base scan.** Builds the directory tree, classifies files into seven categories, counts lines of code, finds large and recently modified files, computes per-directory disk usage. This is the agent's initial picture of the target.
 2. **Survey pass.** A short agent loop (max 3 turns) reads the base scan, describes the target in plain language, and decides which investigation tools are relevant. Tiny targets skip the survey.
 3. **Dir loops.** Every directory gets its own isolated agent loop, leaves-first, with up to 14 turns. The agent has read-only access to the filesystem and a toolbelt of `read_file`, `list_directory`, `run_command`, `parse_structure`, `write_cache`, `think`, `checkpoint`, `flag`, and `submit_report`.
 4. **Cache.** Each file and directory summary is written to `/tmp/luminos/` so subsequent runs on the same target don't re-derive what hasn't changed.
 5. **Context budget guard.** Per-turn `input_tokens` is watched against a budget (currently 70% of the model's context window) so a rogue directory can't blow the context window.
 6. **Final synthesis.** A short agent loop reads the directory-level cache entries (not the raw files) and produces the project-level brief, the detailed analysis, and the severity-ranked flags.
 ## Development
 Run the test suite:
 ```bash
 python3 -m unittest discover -s tests/
 ```
 Modules that are intentionally not unit tested:
 - `luminos_lib/ast_parser.py`: requires tree-sitter grammars installed
 - `luminos_lib/prompts.py`: string templates only
 `luminos_lib/ai.py` is partially covered. End-to-end agent loops require a live Anthropic API and stay exempt, but pure helpers are tested in `tests/test_ai_pure.py`.
 ## License
 Apache License 2.0. See [`LICENSE`](LICENSE) for the full text.
 ## Source of truth
 The canonical home for this project is the [Forgejo repository](https://forgejo.labbity.unbiasedgeek.com/archeious/luminos). The GitHub copy is a read-only mirror, pushed automatically from Forgejo. Issues, pull requests, and the project wiki live on Forgejo.
--- a/docs/externalize.md
+++ b/docs/externalize.md
@ -0,0 +1,36 @@
 # Externalize Protocol
 > Triggered when the user says "externalize" or "externalize your thoughts."
 > This is a STANDALONE action. Do NOT wrap up unless separately asked.
 ## Steps
 1. **Determine session number** — check the Session Log in CLAUDE.md for the
   latest session number, increment by 1
 2. **Pull wiki** — ensure `docs/wiki/` is current:
   ```bash
   git -C docs/wiki pull   # or clone if missing
   ```
 3. **Create session wiki page** — write `docs/wiki/Session{N}.md` with:
   - Date, focus, duration estimate
   - What was done (with detail — reference actual files and commits)
   - Discoveries and observations
   - Decisions made and why
   - Raw Thinking — observations, concerns, trade-offs, and loose threads that
     came up during the session but weren't part of the main deliverable.
     Things you'd mention if pair programming: prerequisites noticed, corners
     being painted into, intent mismatches, unresolved questions.
   - What's next
 4. **Update SessionRetrospectives.md** — read the current index, add the new
   session row, write it back
 5. **Commit and push wiki:**
   ```bash
   cd docs/wiki
   git add -A
   git commit -m "retro: Session {N} — <one-line summary>"
   git push
   ```
--- a/docs/wrap-up.md
+++ b/docs/wrap-up.md
@ -0,0 +1,31 @@
 # Session Wrap-Up Checklist
 > Triggered when the user says "wrap up", "end session", or similar.
 > Always externalize FIRST, then do the steps below.
 ## Steps
 1. **Externalize** — run the `docs/externalize.md` protocol if not already
   done this session
 2. **Reread CLAUDE.md** — ensure you have the latest context before editing
 3. **Update CLAUDE.md:**
   - Update **Current Project State** — phase, last worked on (today's date),
     last commit, blocking issues
   - Update **Session Log** — add new entry, keep only last 3 sessions,
     remove older ones (full history is in the wiki)
 4. **Commit and push main repo:**
   ```bash
   git add CLAUDE.md
   git commit -m "chore: update CLAUDE.md for session {N}"
   git push
   ```
 5. **Verify nothing is unpushed** — both the main repo and docs/wiki should
   have no pending commits
 6. **Recommend next session** — tell the user what the best next session
   should tackle, in priority order based on PLAN.md and any open Forgejo
   issues
--- a/luminos.py
+++ b/luminos.py
@ -16,11 +16,16 @@ from luminos_lib.filetypes import (
 from luminos_lib.code import detect_languages, find_large_files
 from luminos_lib.recency import find_recent_files
 from luminos_lib.disk import get_disk_usage, top_directories
 from luminos_lib.watch import watch_loop
 from luminos_lib.report import format_report
 def _progress(label):
-    """Return (on_file, finish) for in-place per-file progress on stderr."""
+    """Return (on_file, finish) for in-place per-file progress on stderr.
    on_file(path) overwrites the current line with the label and truncated path.
    finish() finalises the line with a newline.
    """
    cols = shutil.get_terminal_size((80, 20)).columns
    prefix = f"  [scan] {label}... "
    available = max(cols - len(prefix), 10)
@ -38,7 +43,7 @@ def _progress(label):
 def scan(target, depth=3, show_hidden=False, exclude=None):
-    """Run the base scan and return the report dict consumed by the AI pass."""
+    """Run all analyses on the target directory and return a report dict."""
    report = {}
    exclude = exclude or []
@ -84,8 +89,7 @@ def main():
    parser = argparse.ArgumentParser(
        prog="luminos",
        description="Luminos — file system intelligence tool. "
-                    "Runs an agentic Claude investigation against a directory "
+                    "Explores a directory and produces a reconnaissance report.",
                    "and produces a reconnaissance report.",
    )
    parser.add_argument("target", nargs="?", help="Target directory to analyze")
    parser.add_argument("-d", "--depth", type=int, default=3,
@ -96,10 +100,17 @@ def main():
                        help="Output report as JSON")
    parser.add_argument("-o", "--output", metavar="FILE",
                        help="Write report to a file")
    parser.add_argument("--ai", action="store_true",
                        help="Use Claude AI to analyze directory purpose "
                             "(requires ANTHROPIC_API_KEY)")
    parser.add_argument("--watch", action="store_true",
                        help="Re-scan every 30 seconds and show diffs")
    parser.add_argument("--clear-cache", action="store_true",
-                        help="Clear the investigation cache (/tmp/luminos/)")
+                        help="Clear the AI investigation cache (/tmp/luminos/)")
    parser.add_argument("--fresh", action="store_true",
-                        help="Force a new investigation (ignore cached results)")
+                        help="Force a new AI investigation (ignore cached results)")
    parser.add_argument("--install-extras", action="store_true",
                        help="Show status of optional AI dependencies")
    parser.add_argument("-x", "--exclude", metavar="DIR", action="append",
                        default=[],
                        help="Exclude a directory name from scan and analysis "
@ -107,8 +118,15 @@ def main():
    args = parser.parse_args()
    # --install-extras: show package status and exit
    if args.install_extras:
        from luminos_lib.capabilities import print_status
        print_status()
        return
    # --clear-cache: wipe /tmp/luminos/ (lazy import to avoid AI deps)
    if args.clear_cache:
-        from luminos_lib.cache import clear_cache
+        from luminos_lib.capabilities import clear_cache
        clear_cache()
        if not args.target:
            return
@ -122,24 +140,25 @@ def main():
              file=sys.stderr)
        sys.exit(1)
    if not os.environ.get("ANTHROPIC_API_KEY"):
        print("luminos requires ANTHROPIC_API_KEY. "
              "Set it with: export ANTHROPIC_API_KEY=your-key-here",
              file=sys.stderr)
        sys.exit(0)
    if args.exclude:
        print(f"  [scan] Excluding: {', '.join(args.exclude)}", file=sys.stderr)
    if args.watch:
        watch_loop(target, depth=args.depth, show_hidden=args.all,
                   json_output=args.json_output)
        return
    report = scan(target, depth=args.depth, show_hidden=args.all,
                  exclude=args.exclude)
-    from luminos_lib.ai import analyze_directory
+    flags = []
-    brief, detailed, flags = analyze_directory(
+    if args.ai:
-        report, target, fresh=args.fresh, exclude=args.exclude)
+        from luminos_lib.ai import analyze_directory
-    report["ai_brief"] = brief
+        brief, detailed, flags = analyze_directory(
-    report["ai_detailed"] = detailed
+            report, target, fresh=args.fresh, exclude=args.exclude)
-    report["flags"] = flags
+        report["ai_brief"] = brief
        report["ai_detailed"] = detailed
        report["flags"] = flags
    if args.json_output:
        output = json.dumps(report, indent=2, default=str)
--- a/luminos_lib/ai.py
+++ b/luminos_lib/ai.py
--- a/luminos_lib/cache.py
+++ b/luminos_lib/cache.py
@ -3,8 +3,6 @@
 import hashlib
 import json
 import os
 import shutil
 import sys
 import uuid
 from datetime import datetime, timezone
@ -12,16 +10,6 @@ CACHE_ROOT = "/tmp/luminos"
 INVESTIGATIONS_PATH = os.path.join(CACHE_ROOT, "investigations.json")
 def clear_cache():
    """Remove all investigation caches under CACHE_ROOT."""
    if os.path.isdir(CACHE_ROOT):
        shutil.rmtree(CACHE_ROOT)
        print(f"Cleared cache: {CACHE_ROOT}", file=sys.stderr)
    else:
        print(f"No cache to clear ({CACHE_ROOT} does not exist).",
              file=sys.stderr)
 def _sha256_path(path):
    """Return a hex SHA-256 of a path string, used as cache key."""
    return hashlib.sha256(path.encode("utf-8")).hexdigest()
--- a/luminos_lib/capabilities.py
+++ b/luminos_lib/capabilities.py
@ -0,0 +1,139 @@
 """Capability detection and cache management for optional luminos dependencies.
 The base tool requires zero external packages. The --ai flag requires:
  - anthropic       (API transport)
  - tree-sitter     (AST parsing via parse_structure tool)
  - python-magic    (improved file classification)
 This module is the single place that knows about optional dependencies.
 """
 _PACKAGES = {
    "anthropic": {
        "import": "anthropic",
        "pip": "anthropic",
        "purpose": "Claude API client (streaming, retries, token counting)",
    },
    "tree-sitter": {
        "import": "tree_sitter",
        "pip": ("tree-sitter tree-sitter-python tree-sitter-javascript "
                "tree-sitter-rust tree-sitter-go"),
        "purpose": "AST parsing for parse_structure tool",
    },
    "python-magic": {
        "import": "magic",
        "pip": "python-magic",
        "purpose": "Improved file type detection via libmagic",
    },
 }
 def _check_package(import_name):
    """Return True if a package is importable."""
    try:
        __import__(import_name)
        return True
    except ImportError:
        return False
 ANTHROPIC_AVAILABLE = _check_package("anthropic")
 TREE_SITTER_AVAILABLE = _check_package("tree_sitter")
 MAGIC_AVAILABLE = _check_package("magic")
 def check_ai_dependencies():
    """Check that all --ai dependencies are installed.
    If any are missing, prints a clear error with the pip install command
    and returns False. Returns True if everything is available.
    """
    missing = []
    for name, info in _PACKAGES.items():
        if not _check_package(info["import"]):
            missing.append(name)
    if not missing:
        return True
    # Also check tree-sitter grammar packages
    grammar_missing = []
    if "tree-sitter" not in missing:
        for grammar in ["tree_sitter_python", "tree_sitter_javascript",
                        "tree_sitter_rust", "tree_sitter_go"]:
            if not _check_package(grammar):
                grammar_missing.append(grammar.replace("_", "-"))
    import sys
    print("\nluminos --ai requires missing packages:", file=sys.stderr)
    for name in missing:
        print(f"  \u2717 {name}", file=sys.stderr)
    for name in grammar_missing:
        print(f"  \u2717 {name}", file=sys.stderr)
    # Build pip install command
    pip_parts = []
    for name in missing:
        pip_parts.append(_PACKAGES[name]["pip"])
    for name in grammar_missing:
        pip_parts.append(name)
    pip_cmd = " \\\n                ".join(pip_parts)
    print(f"\n  Install with:\n    pip install {pip_cmd}\n", file=sys.stderr)
    return False
 def print_status():
    """Print the install status of all optional packages."""
    print("\nLuminos optional dependencies:\n")
    for name, info in _PACKAGES.items():
        available = _check_package(info["import"])
        mark = "\u2713" if available else "\u2717"
        status = "installed" if available else "missing"
        print(f"  {mark} {name:20s} {status:10s}  {info['purpose']}")
    # Grammar packages
    grammars = {
        "tree-sitter-python": "tree_sitter_python",
        "tree-sitter-javascript": "tree_sitter_javascript",
        "tree-sitter-rust": "tree_sitter_rust",
        "tree-sitter-go": "tree_sitter_go",
    }
    print()
    for name, imp in grammars.items():
        available = _check_package(imp)
        mark = "\u2713" if available else "\u2717"
        status = "installed" if available else "missing"
        print(f"  {mark} {name:20s} {status:10s}  Language grammar")
    # Full install command (deduplicated)
    all_pkgs = []
    seen = set()
    for info in _PACKAGES.values():
        for pkg in info["pip"].split():
            if pkg not in seen:
                all_pkgs.append(pkg)
                seen.add(pkg)
    for name in grammars:
        if name not in seen:
            all_pkgs.append(name)
            seen.add(name)
    print(f"\n  Install all with:\n    pip install {' '.join(all_pkgs)}\n")
 from luminos_lib.cache import CACHE_ROOT
 def clear_cache():
    """Remove all investigation caches under /tmp/luminos/."""
    import shutil
    import os
    import sys
    if os.path.isdir(CACHE_ROOT):
        shutil.rmtree(CACHE_ROOT)
        print(f"Cleared cache: {CACHE_ROOT}", file=sys.stderr)
    else:
        print(f"No cache to clear ({CACHE_ROOT} does not exist).",
              file=sys.stderr)
--- a/luminos_lib/prompts.py
+++ b/luminos_lib/prompts.py
@ -209,84 +209,3 @@ Call `submit_survey` exactly once with:
 You have at most 3 turns. In almost all cases you should call
 `submit_survey` on your first turn. Use a second turn only if you
 genuinely need to think before committing."""
 _PLANNING_SYSTEM_PROMPT = """\
 You are an investigation planner. Your job is to decide where to invest
 investigative depth across a directory tree, BEFORE the per-directory
 investigation begins. You allocate turns (agent reasoning steps) to
 directories based on their likely complexity and importance.
 ## Your Task
 Create an investigation plan for the target: {target}
 ## Inputs
 Survey assessment (from a prior reconnaissance pass):
 {survey_context}
 Full directory tree:
 {tree_text}
 File signals:
 {file_signals}
 Total directories to investigate: {dir_count}
 Directories already cached (will be skipped): {cached_dirs}
 ## How to Allocate
 Classify each directory into one of three tiers:
 **priority** (15-20 turns): directories that are likely complex, central,
 or important. Signs: many source files, core application logic, complex
 configuration, entry points, schemas, migrations. These deserve deep
 investigation with multiple tool calls per file.
 **shallow** (5 turns): directories that are simple, peripheral, or
 predictable. Signs: few files, generated/vendored content, test fixtures,
 static assets, documentation-only dirs. A quick pass is sufficient.
 **skip** (0 turns): directories that should be skipped entirely. Signs:
 build output, dependency caches, vendored code, generated artifacts. The
 investigation would waste turns and produce noise.
 Directories you do not mention go into a default tier ({default_turns}
 turns). You do NOT need to list every directory. Focus on the ones where
 the default allocation would clearly be wrong (too many turns for a
 trivial dir, or too few for a complex one).
 ## Investigation Order
 Choose one of these ordering strategies:
 - **leaf-first**: deepest directories first, parents last. This is the
  default and ensures parent directories always have child summaries
  available. Best for most codebases.
 - **priority-first**: priority directories before shallow ones, but
  still leaf-first within each tier. Good when certain subtrees are
  clearly more important and you want findings from them to inform
  the rest of the investigation.
 Both strategies preserve the leaf-first invariant (children before
 parents) to ensure child summaries are available when investigating
 parent directories.
 ## Budget
 The global turn budget is {global_budget} turns across all directories.
 Your allocations should roughly respect this budget, though small
 overages are fine. If you allocate significantly more than the budget,
 the orchestrator will cap individual directories.
 ## Notes Field
 Use `notes` to communicate anything the per-directory agents should
 know that the survey did not capture. Cross-cutting concerns, suspected
 relationships between directories, or investigation priorities. Leave
 empty if you have nothing to add beyond the tier assignments.
 ## Output
 Call `submit_plan` exactly once. You have at most 3 turns, but you
 should almost always submit on your first turn. Use additional turns
 only if you genuinely need to reason through a complex target layout."""
--- a/luminos_lib/watch.py
+++ b/luminos_lib/watch.py
@ -0,0 +1,108 @@
 """Watch mode — re-scan and show diffs every 30 seconds."""
 import json
 import sys
 import time
 import os
 def _snapshot(classified_files):
    """Create a snapshot dict: path -> (size, category)."""
    return {f["path"]: (f["size"], f["category"]) for f in classified_files}
 def _diff_snapshots(old, new):
    """Compare two snapshots and return changes."""
    old_paths = set(old.keys())
    new_paths = set(new.keys())
    added = new_paths - old_paths
    removed = old_paths - new_paths
    common = old_paths & new_paths
    size_changes = []
    for p in common:
        old_size = old[p][0]
        new_size = new[p][0]
        if old_size != new_size:
            size_changes.append((p, old_size, new_size))
    return added, removed, size_changes
 def _human_size(nbytes):
    for unit in ("B", "KB", "MB", "GB"):
        if nbytes < 1024:
            if unit == "B":
                return f"{nbytes} {unit}"
            return f"{nbytes:.1f} {unit}"
        nbytes /= 1024
    return f"{nbytes:.1f} TB"
 def watch_loop(target, depth=3, show_hidden=False, json_output=False):
    """Run scan in a loop, printing diffs between runs."""
    # Import here to avoid circular import
    from luminos_lib.filetypes import classify_files
    print(f"[luminos] Watching {target} (Ctrl+C to stop)")
    print(f"[luminos] Scanning every 30 seconds...")
    print()
    prev_snapshot = None
    try:
        while True:
            classified = classify_files(target, show_hidden=show_hidden)
            current = _snapshot(classified)
            if prev_snapshot is not None:
                added, removed, size_changes = _diff_snapshots(
                    prev_snapshot, current
                )
                if not added and not removed and not size_changes:
                    ts = time.strftime("%H:%M:%S")
                    print(f"[{ts}] No changes detected.")
                else:
                    ts = time.strftime("%H:%M:%S")
                    print(f"[{ts}] Changes detected:")
                    if json_output:
                        diff = {
                            "timestamp": ts,
                            "added": sorted(added),
                            "removed": sorted(removed),
                            "size_changes": [
                                {"path": p, "old_size": o, "new_size": n}
                                for p, o, n in size_changes
                            ],
                        }
                        print(json.dumps(diff, indent=2))
                    else:
                        for p in sorted(added):
                            name = os.path.basename(p)
                            print(f"  + NEW  {name}")
                            print(f"         {p}")
                        for p in sorted(removed):
                            name = os.path.basename(p)
                            print(f"  - DEL  {name}")
                            print(f"         {p}")
                        for p, old_s, new_s in size_changes:
                            name = os.path.basename(p)
                            delta = new_s - old_s
                            sign = "+" if delta > 0 else ""
                            print(f"  ~ SIZE {name}  "
                                  f"{_human_size(old_s)} -> {_human_size(new_s)} "
                                  f"({sign}{_human_size(delta)})")
                    print()
            else:
                print(f"[{time.strftime('%H:%M:%S')}] "
                      f"Initial scan complete: {len(current)} files indexed.")
                print()
            prev_snapshot = current
            time.sleep(30)
    except KeyboardInterrupt:
        print("\n[luminos] Watch stopped.")
--- a/requirements.txt
+++ b/requirements.txt
@ -1,7 +0,0 @@
 anthropic
 python-magic
 tree-sitter
 tree-sitter-python
 tree-sitter-javascript
 tree-sitter-rust
 tree-sitter-go
--- a/setup_env.sh
+++ b/setup_env.sh
@ -2,7 +2,6 @@
 set -euo pipefail
 VENV_DIR="$HOME/luminos-env"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 if [ -d "$VENV_DIR" ]; then
    echo "venv already exists at $VENV_DIR"
@ -14,19 +13,17 @@ fi
 echo "Activating venv..."
 source "$VENV_DIR/bin/activate"
-echo "Installing packages from requirements.txt..."
+echo "Installing packages..."
-pip install -r "$SCRIPT_DIR/requirements.txt"
+pip install anthropic tree-sitter tree-sitter-python \
            tree-sitter-javascript tree-sitter-rust \
            tree-sitter-go python-magic
 echo ""
 echo "Done. To activate the venv in future sessions:"
 echo ""
 echo "  source ~/luminos-env/bin/activate"
 echo ""
-echo "Set your Anthropic API key:"
+echo "Then run luminos as usual:"
 echo ""
-echo "  export ANTHROPIC_API_KEY=your-key-here"
+echo "  python3 luminos.py --ai <target>"
 echo ""
 echo "Then run luminos:"
 echo ""
 echo "  python3 luminos.py <target>"
 echo ""
--- a/tests/test_ai_pure.py
+++ b/tests/test_ai_pure.py
--- a/tests/test_capabilities.py
+++ b/tests/test_capabilities.py
@ -0,0 +1,37 @@
 """Tests for luminos_lib/capabilities.py"""
 import unittest
 from unittest.mock import patch
 from luminos_lib.capabilities import _check_package
 class TestCheckPackage(unittest.TestCase):
    def test_importable_package(self):
        # json is always available in stdlib
        self.assertTrue(_check_package("json"))
    def test_missing_package(self):
        self.assertFalse(_check_package("_luminos_nonexistent_package_xyz"))
    def test_importable_returns_true(self):
        with patch("builtins.__import__", return_value=None):
            # patch doesn't work cleanly here; use a real stdlib module
            pass
        self.assertTrue(_check_package("os"))
    def test_import_error_returns_false(self):
        import builtins
        original_import = builtins.__import__
        def fake_import(name, *args, **kwargs):
            if name == "_fake_missing_module":
                raise ImportError("No module named '_fake_missing_module'")
            return original_import(name, *args, **kwargs)
        with patch("builtins.__import__", side_effect=fake_import):
            self.assertFalse(_check_package("_fake_missing_module"))
 if __name__ == "__main__":
    unittest.main()