Plan step

.idea/Agents.iml

@@ -5,6 +5,7 @@
       <sourceFolder url="file://$MODULE_DIR$" isTestSource="false" />
       <sourceFolder url="file://$MODULE_DIR$/agents/issue_triage/tests" isTestSource="true" />
       <excludeFolder url="file://$MODULE_DIR$/.venv" />
+      <excludeFolder url="file://$MODULE_DIR$/projects/agents" />
     </content>
     <orderEntry type="jdk" jdkName="Python 3.14 (Agents)" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />

.idea/webResources.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="WebResourcesPaths">
+    <contentEntries>
+      <entry url="file://$PROJECT_DIR$">
+        <entryData>
+          <resourceRoots>
+            <path value="file://$PROJECT_DIR$/projects" />
+          </resourceRoots>
+        </entryData>
+      </entry>
+    </contentEntries>
+  </component>
+</project>

CHANGELOG.md

@@ -1,3 +1,8 @@
+### 2026-09-23
+1. Add memory for Agent - memory dir. Not count timestamps, need work
+2. Add FileSelection - file graph is converting to consumable table, works for small amount of files
+3. Refactor planification prompt - it is better now
+
 ### 2026-09-22
 1. Add verification step - ensure the issue can be solved by coding
 2. Add repo download step

agents/codebase_analyst/entrypoint.py

@@ -25,11 +25,11 @@ import os
 from pathlib import Path
 from typing import List, Literal, Optional, Type, TypeVar
 
-from pydantic import BaseModel, Field, ValidationError, TypeAdapter
+from pydantic import BaseModel, Field, ValidationError, TypeAdapter, field_validator
 
-from agents.coders.repo import RepoContext
-from common.llm_client import LLMClient
-from contracts.RepoContext import Language, LanguageLiteral
+from common.llm_client import LLMClient, ResponseCache
+from contracts.RepoContext import RepoContext
+from contracts.CodeLanguages import Language, LanguageLiteral
 from contracts.coders.VerifyOutput import sanitize_for_openai
 
 log = logging.getLogger("entrypoint_analyzer")
@@ -86,10 +86,21 @@ class Attempt(BaseModel):
 
 class AnalysisResult(BaseModel):
     language: Language
-    entrypoint: str
+    entrypoint: str = Field(
+        ...,
+        description="Relative path from repo_path to the entrypoint file",
+    )
     attempts: List[Attempt]
     reasoning: str
 
+    @field_validator("entrypoint")
+    @classmethod
+    def entrypoint_must_exist(cls, v: str, info) -> str:
+        repo = info.data.get("repo_path")
+        if repo and not (repo / v).is_file():
+            raise ValueError(f"Entrypoint not found: {repo / v}")
+        return v
+
 
 # --------------------------------------------------------------------------- #
 # LLM plumbing: LLMClient wrapper with strict schema + cache + retries         #
@@ -97,41 +108,6 @@ class AnalysisResult(BaseModel):
 
 T = TypeVar("T", bound=BaseModel)
 
-
-class ResponseCache:
-    """File-backed cache: prompt-hash -> validated-model JSON. Makes runs idempotent."""
-
-    def __init__(self, path: Optional[Path] = None) -> None:
-        self.path = path
-        self._mem: dict[str, str] = {}
-        if path and path.exists():
-            try:
-                self._mem = json.loads(path.read_text("utf-8"))
-            except Exception:  # noqa: BLE001
-                log.warning("Corrupt cache at %s; starting fresh", path)
-
-    @staticmethod
-    def key(system: str, user: str, schema: Type[BaseModel]) -> str:
-        h = hashlib.sha256()
-        h.update(schema.__name__.encode())
-        h.update(b"\x00")
-        h.update(system.encode())
-        h.update(b"\x00")
-        h.update(user.encode())
-        return h.hexdigest()
-
-    def get(self, k: str) -> Optional[str]:
-        return self._mem.get(k)
-
-    def put(self, k: str, v: str) -> None:
-        self._mem[k] = v
-        if self.path:
-            self.path.parent.mkdir(parents=True, exist_ok=True)
-            tmp = self.path.with_suffix(self.path.suffix + ".tmp")
-            tmp.write_text(json.dumps(self._mem, indent=2, sort_keys=True), "utf-8")
-            tmp.replace(self.path)
-
-
 class StructuredLLM:
     """
     Wrap the project's `LLMClient` with:
@@ -404,6 +380,7 @@ class EntrypointAnalyzer:
 
 
 def gather_repo_entrypoint(llm: LLMClient, repo: RepoContext, cache_path: Optional[str] = None) -> AnalysisResult:
+    log.debug("Gathering repo entrypoint")
     return EntrypointAnalyzer(
         StructuredLLM(llm, cache=ResponseCache(Path(cache_path)) if cache_path else None)
     ).analyze(Path(repo.repo_dir))

agents/codebase_analyst/graph_tool.py

@@ -1,10 +1,13 @@
 import json
+import logging
+import os
+import pickle
 import shutil
 import subprocess
 from abc import ABC, abstractmethod
 from functools import partial
 from pathlib import Path
-from typing import Optional, Callable
+from typing import Optional, Callable, TypedDict, Generic, Hashable, TypeVar
 
 import networkx as nx
 import pandas as pd
@@ -12,9 +15,16 @@ from networkx.algorithms.community import louvain_communities
 
 from pydantic import BaseModel, Field, ValidationError
 
+from agents.codebase_analyst.entrypoint import gather_repo_entrypoint
 from common.llm_client import LLMClient
-from contracts.RepoContext import Language, ToolRequirement, DependencyGraph, DependencyNode, DependencyEdge, \
-    AnalysisResult, AnalysisInput, AnalysisError
+from contracts.GraphAnalyzer import AnalyzeResult, DependencyEdge, DependencyNode
+from contracts.RepoContext import Language, ToolRequirement, DependencyGraph, \
+    AnalysisResult, AnalysisInput, AnalysisError, RepoContext
+from contracts.coders.RunContext import RunContext
+
+
+logger = logging.getLogger("graph_tool")
+logger.setLevel(logging.DEBUG)
 
 
 def find_tool(command: str) -> Optional[str]:
@@ -452,7 +462,8 @@ class JavaAdapter(LanguageAdapter):
             raise RuntimeError(f"gradle dependencies failed: {result.stderr.strip()}")
         return self._parse_tree_text(result.stdout, entrypoint)
 
-    def _parse_tree_text(self, text: str, entrypoint: str) -> DependencyGraph:
+    @staticmethod
+    def _parse_tree_text(text: str, entrypoint: str) -> DependencyGraph:
         # Simplified parser for the textual tree format.
         # In production, use the JSON output of the Maven/Gradle plugin.
         nodes: list[DependencyNode] = []
@@ -636,7 +647,30 @@ ADAPTER_REGISTRY: dict[Language, AdapterFactory] = {
 }
 
 
-def analyze_repository(inp: AnalysisInput) -> AnalysisResult:
+def analyze_repo_with_cache(run_ctx: RunContext, repo: RepoContext) -> AnalysisResult:
+    repo_analyze = None
+    analysis_cache_path = run_ctx.config.project_mem_dir() / "repo_analysis.json"
+    if os.path.exists(analysis_cache_path):
+        try:
+            repo_analyze = pickle.load(open(analysis_cache_path, "rb"))
+            logger.debug("repo analysis from cache")
+        except Exception as e:
+            print(e)
+            pass
+
+    if not repo_analyze:
+        logger.debug("generating repo analysis")
+        repo_analyze = analyze_repository(AnalysisInput(
+            repo=repo
+        ), run_ctx)
+        if repo_analyze.error:
+            raise BaseException(repo_analyze.error)
+        with open(analysis_cache_path, "wb") as f:
+            pickle.dump(repo_analyze, f)
+
+    return repo_analyze
+
+def analyze_repository(inp: AnalysisInput, run_ctx: RunContext) -> AnalysisResult:
     """
     Idempotent entry point.
 
@@ -644,15 +678,19 @@ def analyze_repository(inp: AnalysisInput) -> AnalysisResult:
     (either a graph or a structured error). No files are written to the
     repository under analysis.
     """
-    adapter_factory = ADAPTER_REGISTRY.get(inp.language)
+    entrypoint_analyze = gather_repo_entrypoint(run_ctx.llm, inp.repo, run_ctx.config.project_mem_dir() / "entrypoint.json")
+    language = entrypoint_analyze.language
+    entrypoint = entrypoint_analyze.entrypoint
+
+    adapter_factory = ADAPTER_REGISTRY.get(language)
     if adapter_factory is None:
         return AnalysisResult(
             success=False,
             error=AnalysisError(
                 error_code="UNSUPPORTED_LANGUAGE",
-                message=f"No adapter registered for language '{inp.language}'",
-                language=inp.language,
-                entrypoint=inp.entrypoint,
+                message=f"No adapter registered for language '{language}'",
+                language=language,
+                entrypoint=entrypoint,
             ),
         )
 
@@ -670,27 +708,27 @@ def analyze_repository(inp: AnalysisInput) -> AnalysisResult:
             error=AnalysisError(
                 error_code="MISSING_TOOL",
                 message=(
-                    f"Cannot build dependency graph for '{inp.language.value}': "
+                    f"Cannot build dependency graph for '{language.value}': "
                     f"required tool(s) not found on PATH: "
                     f"{', '.join(r.tool_name for r in missing)}"
                 ),
                 missing_tools=missing,
-                language=inp.language,
-                entrypoint=inp.entrypoint,
+                language=language,
+                entrypoint=entrypoint,
             ),
         )
 
     # --- Build graph ---
     try:
-        graph = adapter.build_graph(inp.repo_path, inp.entrypoint)
+        graph = adapter.build_graph(inp.repo.repo_dir, entrypoint)
     except subprocess.TimeoutExpired:
         return AnalysisResult(
             success=False,
             error=AnalysisError(
                 error_code="TOOL_TIMEOUT",
-                message=f"Tool timed out while analyzing {inp.entrypoint}",
-                language=inp.language,
-                entrypoint=inp.entrypoint,
+                message=f"Tool timed out while analyzing {entrypoint}",
+                language=language,
+                entrypoint=entrypoint,
             ),
         )
     except Exception as exc:
@@ -699,39 +737,45 @@ def analyze_repository(inp: AnalysisInput) -> AnalysisResult:
             error=AnalysisError(
                 error_code="ANALYSIS_FAILED",
                 message=str(exc),
-                language=inp.language,
-                entrypoint=inp.entrypoint,
+                language=language,
+                entrypoint=entrypoint,
             ),
         )
 
-    G_all = to_networkx(graph, include_external=True)
     G = to_networkx(graph, include_external=False)  # internal-only analysis
     res_internal = analyze(G, graph, label="_internal")
-    res_all = analyze(G_all, graph, label="_all")
-    leaf_clusters = cluster_leaves(G, res_internal["leaf_no_deps"])
+    leaf_clusters = cluster_leaves(G, res_internal.leaf_no_deps)
+
+    res_all = analyze(to_networkx(graph, include_external=True), graph, label="_all")
 
     return AnalysisResult(success=True, graph=graph, res_all=res_all, leaf_clusters=leaf_clusters)
 
 
-def to_networkx(dep_graph: DependencyGraph, include_external=False):
+def to_networkx(dep_graph: "DependencyGraph", include_external: bool = False) -> nx.DiGraph[DependencyNode]:
+    """
+    Convert a DependencyGraph into a networkx DiGraph.
+
+    Nodes are identified by their string id. Edges point from the source
+    (the file that declares the dependency) to the target (the file that
+    is depended upon).
+
+    If include_external is False, external nodes (and edges touching them)
+    are omitted.
+    """
     G = nx.DiGraph()
 
-    # Nodes
+    id_to_node: dict[str, DependencyNode] = {}
     for n in dep_graph.nodes:
         if not include_external and n.is_external:
             continue
-        G.add_node(n.id, label=n.label, language=n.language.value, is_external=n.is_external)
+        G.add_node(n)  # DependencyNode must be hashable
+        id_to_node[n.id] = n
 
-    # Edges (source depends on target)
     for e in dep_graph.edges:
-        if e.source in G and e.target in G:
-            G.add_edge(e.source, e.target, kind=e.kind)
-
-    # Add isolated internal files that never appear in edges
-    if not include_external:
-        for n in dep_graph.nodes:
-            if not n.is_external and n.id not in G:
-                G.add_node(n.id, label=n.label, language=n.language.value, is_external=False)
+        src = id_to_node.get(e.source)
+        tgt = id_to_node.get(e.target)
+        if src is not None and tgt is not None:
+            G.add_edge(src, tgt, kind=e.kind)
 
     return G
 
@@ -741,54 +785,66 @@ def package_of(path: str) -> str:
 
 
 COLS = [
-    "file", "language", "in_degree", "out_degree",
+    "file", "in_degree", "out_degree",
     "isolated", "leaf_no_deps", "entry_no_dependents",
     "used_by_files", "used_by_packages", "community",
 ]
 
 
-def analyze(G, graph, label=""):
-    in_deg  = dict(G.in_degree())
-    out_deg = dict(G.out_degree())
+def analyze(
+    G: nx.DiGraph[DependencyNode],
+    graph: DependencyGraph,          # NOTE: currently unused in the body
+    label: str = "",
+) -> AnalyzeResult:
+    in_deg: dict[DependencyNode, int] = dict(G.in_degree())
+    out_deg: dict[DependencyNode, int] = dict(G.out_degree())
 
     # 1. Truly isolated: no in and no out edges
-    isolated = [n for n in G if G.degree(n) == 0]
+    isolated: list[DependencyNode] = [n for n in G if G.degree(n) == 0]
 
     # 2. Leaf: depends on nothing
-    leaf_no_deps = [n for n in G if G.out_degree(n) == 0]
+    leaf_no_deps: list[DependencyNode] = [n for n in G if G.out_degree(n) == 0]
 
     # 3. Entrypoint: nothing depends on it
-    entry_no_dependents = [n for n in G if G.in_degree(n) == 0]
+    entry_no_dependents: list[DependencyNode] = [n for n in G if G.in_degree(n) == 0]
 
     # 4. Widely used: how many distinct files depend on it
-    widely_used = sorted(in_deg.items(), key=lambda kv: kv[1], reverse=True)
+    widely_used: list[tuple[DependencyNode, int]] = sorted(
+        in_deg.items(), key=lambda kv: kv[1], reverse=True
+    )
 
     # 5. How many distinct packages depend on it
-    pkg = {n: package_of(n) for n in G}
-    used_by_packages = {
+    pkg: dict[DependencyNode, Hashable] = {n: package_of(n.id) for n in G}
+    used_by_packages: dict[DependencyNode, int] = {
         n: len({pkg[p] for p in G.predecessors(n)}) for n in G
     }
 
     # 6. Weakly connected components = isolated groups
-    wccs = sorted(nx.weakly_connected_components(G), key=len, reverse=True)
+    wccs: list[set[DependencyNode]] = sorted(
+        nx.weakly_connected_components(G), key=len, reverse=True
+    )
 
     # 7. Strongly connected components = cycles / tightly coupled groups
-    sccs = sorted(
+    sccs: list[set[DependencyNode]] = sorted(
         (c for c in nx.strongly_connected_components(G) if len(c) > 1),
-        key=len, reverse=True,
+        key=len,
+        reverse=True,
     )
 
     # 8. Communities via Louvain
-    U = G.to_undirected()
-    comms = louvain_communities(U, seed=42) if U.number_of_edges() else []
-    node2comm = {n: i for i, c in enumerate(comms) for n in c}
+    U: nx.Graph[DependencyNode] = G.to_undirected()
+    comms: list[set[DependencyNode]] = (
+        louvain_communities(U, seed=42) if U.number_of_edges() else []
+    )
+    node2comm: dict[DependencyNode, int] = {
+        n: i for i, c in enumerate(comms) for n in c
+    }
 
     # Per-file table
-    rows = []
+    rows: list[dict[str, object]] = []
     for n, data in G.nodes(data=True):
         rows.append({
-            "file": n,
-            "language": data.get("language"),
+            "file": n.id,
             "in_degree": in_deg[n],
             "out_degree": out_deg[n],
             "isolated": G.degree(n) == 0,
@@ -808,27 +864,27 @@ def analyze(G, graph, label=""):
     df.to_csv(f"file_metrics{label}.csv", index=False)
 
     pd.DataFrame([
-        {"group_id": i, "size": len(c), "members": ";".join(sorted(c))}
+        {"group_id": i, "size": len(c), "members": ";".join(sorted(n.id for n in c))}
         for i, c in enumerate(wccs)
     ]).to_csv(f"isolated_groups{label}.csv", index=False)
 
     pd.DataFrame([
-        {"scc_id": i, "size": len(c), "members": ";".join(sorted(c))}
+        {"scc_id": i, "size": len(c), "members": ";".join(sorted(n.id for n in c))}
         for i, c in enumerate(sccs)
     ]).to_csv(f"cycles{label}.csv", index=False)
 
-    return {
-        "df": df,
-        "isolated": isolated,
-        "leaf_no_deps": leaf_no_deps,
-        "entry_no_dependents": entry_no_dependents,
-        "widely_used": widely_used,
-        "used_by_packages": used_by_packages,
-        "wccs": wccs,
-        "sccs": sccs,
-        "node2comm": node2comm,
-        "comms": comms,
-    }
+    return AnalyzeResult(
+        df=df,
+        isolated=isolated,
+        leaf_no_deps=leaf_no_deps,
+        entry_no_dependents=entry_no_dependents,
+        widely_used=widely_used,
+        used_by_packages=used_by_packages,
+        wccs=wccs,
+        sccs=sccs,
+        node2comm=node2comm,
+        comms=comms,
+    )
 
 
 def cluster_leaves(G, leaves):

agents/codebase_analyst/select_files.py

@@ -0,0 +1,262 @@
+# steps/select_files.py
+from __future__ import annotations
+
+import json
+import re
+from dataclasses import dataclass
+
+import pandas as pd
+from pydantic import TypeAdapter, ValidationError
+
+from contracts.coders.FileSelection import FileSelectionOutput, FileSelection
+from contracts.coders.GatherOutput import GatherOutput
+
+SelectionAdapter = TypeAdapter(FileSelectionOutput)
+
+
+SYSTEM_PROMPT = """\
+You select the files a coding agent should read to plan a change.
+
+You will receive:
+1. The issue (title, body, acceptance criteria).
+2. A table of repository files with structural metadata.
+3. Column definitions.
+
+Your job: pick the files the agent needs, split into three roles:
+
+- **primary**: files that almost certainly need edits for this task. If the \
+  task says "add X to the user settings page", the settings page component \
+  is primary. Be conservative — include only files you'd bet will be edited.
+- **context**: files needed to understand primary files — imports they rely \
+  on, type definitions they use, config they read. Include if a planner would \
+  be confused without them.
+- **test**: existing tests that cover the primary files. Include even if the \
+  task doesn't mention tests; the agent needs to know what already exists.
+
+Rules:
+- Choose ONLY from the paths in the table. Do not invent paths.
+- For each file, the reason MUST quote or paraphrase a specific identifier, \
+  module name, or phrase from the issue. If you can't write such a reason, \
+  do not select the file.
+- Prefer fewer, higher-confidence selections over many low-confidence ones. \
+  A bad selection wastes context; a missing file causes a bad plan.
+- High `in` means the file is imported by many others — useful context, but \
+  rarely the file to edit. Do not select a file just because `in` is high.
+- Files in the same `community` as a primary file are often related; use \
+  this as a signal, not a rule.
+- `[test]`-prefixed files are tests. Use them to populate the test role.
+- At most 30 selections total.
+
+Output JSON matching the schema. No prose.
+"""
+
+
+@dataclass(frozen=True)
+class SelectFilesInput:
+    gather: GatherOutput
+    table: str                  # pre-formatted, pre-filtered table text
+    filtered_out_count: int     # for the notes
+
+
+def select_files(
+    inp: SelectFilesInput,
+    *,
+    llm,
+) -> FileSelectionOutput:
+    prompt = _build_user_prompt(inp)
+    schema = SelectionAdapter.json_schema()
+
+    raw = llm.chat_with_schema(
+        prompt,
+        {
+            "type": "json_schema",
+            "json_schema": {
+                "name": "FileSelectionOutput",
+                "schema": schema,
+                "strict": True,
+            },
+        },
+        system=SYSTEM_PROMPT,
+    )
+
+    raw = _ensure_dict(raw)
+    try:
+        out = SelectionAdapter.validate_python(raw)
+    except ValidationError as e:
+        raise SelectionError(str(e)) from e
+
+    return _validate_against_table(out, inp.table)
+
+
+# ── prompt ─────────────────────────────────────────────────────
+
+def _build_user_prompt(inp: SelectFilesInput) -> str:
+    g = inp.gather
+    issue = g.issue_context
+
+    parts: list[str] = []
+    parts.append(f"# Issue {issue.issue_id}: {issue.title}")
+    parts.append("")
+    parts.append(issue.body.strip() or "(empty)")
+    parts.append("")
+    if issue.acceptance_criteria:
+        parts.append("## Acceptance criteria")
+        for i, ac in enumerate(issue.acceptance_criteria, 1):
+            parts.append(f"{i}. {ac}")
+        parts.append("")
+
+    parts.append("## Column definitions")
+    parts.append("- `path`: repo-relative path (authoritative)")
+    parts.append("- `lang`: language")
+    parts.append("- `in`: number of files that import this file (in-degree)")
+    parts.append("- `out`: number of files this file imports (out-degree)")
+    parts.append("- `pkg`: number of packages that depend on this file")
+    parts.append("- `comm`: cluster id; files with the same id tend to be "
+                 "related by construction")
+    parts.append("")
+
+    parts.append("## Files")
+    parts.append("```")
+    parts.append(inp.table)
+    parts.append("```")
+    parts.append("")
+
+    if inp.filtered_out_count:
+        parts.append(
+            f"({inp.filtered_out_count} additional files were pre-filtered "
+            f"out as clearly unrelated. Do not select them.)"
+        )
+
+    parts.append("Select the files. Return ONLY the JSON object.")
+    return "\n".join(parts)
+
+
+# ── validation ─────────────────────────────────────────────────
+
+class SelectionError(ValueError):
+    """LLM output violated the selection contract."""
+
+
+def _validate_against_table(
+    out: FileSelectionOutput,
+    table: str,
+) -> FileSelectionOutput:
+    """
+    Reject selections that reference paths not in the table.
+    LLMs hallucinate paths surprisingly often, especially on large tables.
+    """
+    valid_paths = _paths_from_table(table)
+    bad = [s.path for s in out.selections if s.path not in valid_paths]
+    if bad:
+        raise SelectionError(
+            f"LLM selected paths not in the table: {bad[:5]}"
+            + (f" (+{len(bad)-5} more)" if len(bad) > 5 else "")
+        )
+    # dedupe in case the model repeated a path with different roles
+    seen: dict[str, FileSelection] = {}
+    for s in out.selections:
+        if s.path not in seen or s.confidence > seen[s.path].confidence:
+            seen[s.path] = s
+    deduped = list(seen.values())
+    return FileSelectionOutput(selections=deduped, notes=out.notes)
+
+
+def _paths_from_table(table: str) -> set[str]:
+    paths = set()
+    for line in table.splitlines()[1:]:        # skip header
+        first = line.split(" | ", 1)[0].strip()
+        if first.startswith("[test] "):
+            first = first[len("[test] "):]
+        paths.add(first)
+    return paths
+
+
+def _ensure_dict(raw):
+    if isinstance(raw, str):
+        return json.loads(raw)
+    return raw
+
+RENAMES = {
+    "file": "path",
+    "in_degree": "in",
+    "out_degree": "out",
+    "used_by_packages": "pkg",
+    "community": "comm",
+}
+
+# Columns actually used by the LLM. Everything else is either redundant
+# (isolated, leaf_no_deps, entry_no_dependents) or unused (label,
+# used_by_files — a duplicate of in_degree).
+KEEP = list(RENAMES.keys())
+
+
+_TEST_PATH_RE = re.compile(
+    r"(^|/)(tests?|__tests__|spec)(/|$)"      # tests/, test/, __tests__/, spec/
+    r"|(^|/)test_[^/]+\.py$"                   # test_foo.py
+    r"|_test\.(py|go)$"                        # foo_test.py, foo_test.go
+    r"|\.(test|spec)\.(ts|tsx|js|jsx)$",       # foo.test.ts, foo.spec.tsx
+    re.IGNORECASE,
+)
+
+
+def is_test_path(path: str) -> bool:
+    return bool(_TEST_PATH_RE.search(path))
+
+
+def _force_int(series: pd.Series) -> pd.Series:
+    """
+    Coerce any pandas dtype to a plain int64 numpy array wrapped in a Series.
+    Handles Categorical (ordered or not), Int64 (nullable), float with NaN,
+    object with strings, and boolean.
+    """
+    if isinstance(series.dtype, pd.CategoricalDtype):
+        # cat.codes is always plain int8/int16/... — no ordering needed.
+        return pd.Series(series.cat.codes, index=series.index, dtype="int64")
+
+    # For everything else, let pandas convert, then force int64.
+    return (
+        pd.to_numeric(series, errors="coerce")
+        .fillna(0)
+        .astype("int64")
+        .reset_index(drop=True)
+        .set_axis(series.index)
+    )
+
+
+def format_table(df: pd.DataFrame) -> str:
+    """
+    Render the dependency-graph DataFrame as a compact, pipe-separated
+    table suitable for an LLM prompt.
+
+    - Keeps only the columns the model needs.
+    - Renames them to short forms.
+    - Sorts by (community, path) so related files cluster visually.
+    - Prefixes test paths with [test] so the model doesn't have to guess.
+    - Returns the header line + rows as a single string.
+    """
+    if df.empty:
+        return "path | in | out | pkg | comm"
+
+    cols = [c for c in KEEP if c in df.columns]
+    view = df[cols].rename(columns=RENAMES).copy()
+
+    # ── 1. Force every column to a plain Python type ──────────
+    # This is the step that guarantees sort_values never sees a
+    # Categorical, nullable Int64, or object-with-NaN.
+    view["path"] = view["path"].astype(str)
+    for col in ("in", "out", "pkg", "comm"):
+        view[col] = _force_int(view[col])
+
+    view = view.sort_values(["comm", "path"], kind="stable")
+
+    view["path"] = view["path"].map(
+        lambda p: f"[test] {p}" if is_test_path(p) else p
+    )
+
+    header = "path | lang | in | out | pkg | comm"
+    view = view.astype(object).where(pd.notna(view), None)
+    rows = [
+        " | ".join("" if v is None else str(v) for v in row)
+        for row in view.itertuples(index=False, name=None)
+    ]
+    return "\n".join([header, *rows])

agents/coders/BaseCoder.py

@@ -10,7 +10,7 @@ from agents.coders.steps.verify import handle_verify
 from agents.issue_triage.context_builder import YouTrackContextBuilder
 from agents.registry import agent, AgentRegistry
 from common.gitea_mcp_client import GiteaMCPClient
-from common.llm_client import LLMClient
+from common.llm_client import LLMClient, ResponseCache
 from common.youtrack_mcp_client import YouTrackMCPClient
 from contracts.IssueContext import IssueContext
 from contracts.coders.RunContext import RunContext, new_run_id, AgentConfig
@@ -60,10 +60,14 @@ class CoderAgent:
                 gitea=self.gitea_mcp,
                 state=gather_result.state,
                 config=AgentConfig(
-                    youtrack_project=issue_ctx.issue_id.split(":")[0],
-                    gitea_repo=""
+                    agent_dir=Path(__file__).resolve().parents[2] / "projects" / "agents" / self.id,
+                    youtrack_project=issue_ctx.issue_id.split("-")[0],
+                    git_name = "zarch",
+                    git_email = "zarch@zaek.eu"
                 ),
             )
+            run_ctx.llm.cache = ResponseCache(run_ctx.config.project_mem_dir() / "init.json")
+
             step = await handle_verify(
                 VerifyPossibilityInput(gather_result),
                 run_ctx
@@ -73,7 +77,7 @@ class CoderAgent:
 
             step = await handle_plan(
                 PlanInput(gather_result, step.output),
-                llm=self.llm,
+                run_ctx=run_ctx
             )
             print(step)
 

agents/coders/repo.py

@@ -1,26 +1,9 @@
-import os
 import re
 import subprocess
-from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Optional
 
-
-@dataclass
-class RepoContext:
-    """Result object carrying all info a coding agent needs."""
-    repo_dir: Path
-    remote_url: str
-    branch: str
-    base_branch: str
-    head_commit: str
-    is_new_clone: bool
-    is_new_branch: bool
-    original_branch: Optional[str] = None
-    uncommitted_changes: Optional[str] = None  # git diff (tracked)
-    untracked_files: list[str] = field(default_factory=list)
-    stash_ref: Optional[str] = None
-    env: dict = field(default_factory=dict)
+from contracts.RepoContext import RepoContext
 
 
 def _run(cmd: list[str], cwd: Path | None = None, check: bool = True) -> subprocess.CompletedProcess:

agents/coders/steps/plan.py

@@ -3,54 +3,101 @@ from __future__ import annotations
 
 import json
 from dataclasses import dataclass
+from pathlib import Path
 
 from pydantic import TypeAdapter, ValidationError
 
-from agents.codebase_analyst.entrypoint import gather_repo_entrypoint
-from agents.codebase_analyst.graph_tool import analyze_repository
-from agents.coders.repo import ensure_repo_ready, RepoContext
-from common.llm_client import LLMClient
-from contracts.RepoContext import AnalysisInput
+from agents.codebase_analyst.graph_tool import analyze_repo_with_cache
+from agents.codebase_analyst.select_files import format_table, select_files, SelectFilesInput
+from agents.coders.repo import ensure_repo_ready
 from contracts.coders.GatherOutput import GatherOutput
 from contracts.coders.PlanOutput import PlanOutput
+from contracts.coders.RunContext import RunContext
 from contracts.coders.VerifyOutput import FeasibleVerdict
 
 PlanAdapter = TypeAdapter(PlanOutput)
 
 
 SYSTEM_PROMPT = """\
-You are a senior engineer writing an implementation plan for a coding agent.
+You are a senior engineer writing an implementation plan that a coding agent \
+will execute file-by-file.
 
-You will receive an issue (title, body, acceptance criteria, comments), a \
-repository context, the feasibility verdict from a prior triage, and a list \
-of files linked from the issue.
+## Inputs
 
-Produce a plan with these properties:
+You receive:
+- The issue: title, body, acceptance criteria, comments.
+- Repository context: remote URL, default branch.
+- A feasibility verdict from a prior triage step, with reasoning and confidence.
+- Files linked from the issue, with line numbers and per-file confidence.
 
-1. **One step per file.** Each step describes a single file change. If two \
-   files must change together, that's two steps.
+The feasibility verdict is final. Do not re-derive it, do not argue with it, \
+do not mention it in the plan. It is context, not a question.
 
-2. **Commit to a language.** Infer the primary language from the repository \
-   context and the files you plan to touch. Choose the test runner, formatter, \
-   and linter idiomatic to that language. Populate `language` accordingly.
+## Output
 
-3. **Target files, not file contents.** Describe *what* changes in each file, \
-   not the code itself. The Act step writes the code; you decide the shape.
+Return ONLY a JSON object matching the schema at the end of this message. No \
+prose, no markdown fences, no commentary outside the JSON.
 
-4. **Be honest about breaking changes.** Set `breaks_existing=true` only if \
-   the change modifies behavior that callers or users rely on: public API \
-   changes, schema changes, config default changes, removal of features. \
-   Pure additions, bug fixes, and internal refactors are NOT breaking.
+## Plan shape
 
-5. **Risk notes.** If `breaks_existing=true`, list the specific risks. If not, \
-   you may still add notes for reviewer attention (migrations, security, \
-   performance), but this is optional.
+A plan is an ordered list of steps. Each step targets exactly one file. After \
+applying a step the repo should still parse and build — if it wouldn't, split \
+the step.
+
+Order steps so no step depends on code a later step will write. Independent \
+steps go smallest-blast-radius first.
+
+Each step must contain:
+- `file`: repo-relative path. For a new file, mark it as such.
+- `change`: 1–4 sentences a reviewer would understand. Name the symbols being \
+  added, modified, or removed. Do NOT paste code — the Act step writes it. You \
+  may name signatures, types, or schema fields where ambiguity matters.
+- `breaks_existing`: see below.
+- `risk_notes`: required when `breaks_existing=true`; otherwise optional \
+  reviewer notes (migrations, security, perf).
+- `verifies`: how we'll know this step worked — a test to run, a file to check, \
+  a command. If nothing automated applies, write `"manual review"`.
+
+## Acceptance-criteria coverage
+
+Every acceptance criterion must be satisfied by at least one step. Before \
+finalizing, walk the AC list and confirm coverage. If an AC cannot be satisfied \
+by a code change (e.g. "get sign-off"), record it in `uncoverable_criteria` \
+rather than inventing a step for it.
+
+## Language and tooling
+
+Infer the primary language from the repo context and the files you plan to \
+touch. Set `language` accordingly, and pick the test runner, formatter, and \
+linter idiomatic to that language. In a polyglot repo, set `language` to the \
+majority language and use a per-step language override where steps differ.
+
+## Breaking changes
+
+Set `breaks_existing=true` only for:
+- public API changes (signature, return type, thrown errors)
+- schema or data-format changes
+- config default changes
+- feature removal
+
+Pure additions, bug fixes, and internal refactors are NOT breaking. When in \
+doubt, prefer `false` and add a `risk_notes` entry. A false positive here costs \
+more than a false negative.
+
+## Gaps and ambiguity
+
+If the issue is ambiguous or the linked files don't cover the surface area, do \
+not invent. Add a step whose `change` is "investigate X before proceeding" with \
+`file: null`, or populate `open_questions`. A plan that flags uncertainty is \
+more useful than one that looks complete.
+
+## Constraints
 
-Rules:
 - Do not plan to modify files outside the repository.
-- Do not invent files that clearly don't exist unless the plan is to create them.
+- Do not reference files you haven't seen, unless the step creates them.
 - Prefer the smallest plan that satisfies the acceptance criteria.
-- Return ONLY valid JSON matching the schema.
+- Do not restate the issue. The reader has it.
+
 """
 
 
@@ -64,7 +111,7 @@ class PlanInput:
     feasibility: FeasibleVerdict
 
 
-async def handle_plan(inp: PlanInput, *, llm: LLMClient) -> PlanOutput:
+async def handle_plan(inp: PlanInput, *, run_ctx: RunContext) -> PlanOutput:
     if not inp.gather.issue_context.project or len(inp.gather.issue_context.project.repos) == 0:
         raise "No project repo"
 
@@ -74,23 +121,24 @@ async def handle_plan(inp: PlanInput, *, llm: LLMClient) -> PlanOutput:
         "zarch_" + inp.gather.issue_context.issue_id,
         inp.gather.issue_context.project.repos[0].base_branch,
         author_name="zarch",
-        author_email="zarch@zaek.eu"
+        author_email="zarch@zaek.eu",
     )
-    entrypoint_analyze = gather_repo_entrypoint(llm, repo)
-    repo_analyze = analyze_repository(AnalysisInput(
-        repo_path=repo.repo_dir,
-        language=entrypoint_analyze.language,
-        entrypoint=entrypoint_analyze.entrypoint,
-    ))
 
-    if repo_analyze.error:
-        raise repo_analyze.error
-    print(repo_analyze)
+    repo_analyze = analyze_repo_with_cache(run_ctx, repo)
+    selected_files = select_files(
+        SelectFilesInput(
+            inp.gather,
+            format_table(repo_analyze.res_all.df.drop(columns=[c for c in {"leaf_no_deps", "isolated", "entry_no_dependents", "language"} if
+                                          c in repo_analyze.res_all.df.columns])),
+            0
+        ),
+        llm=run_ctx.llm
+    )
+    print(selected_files)
 
-    prompt = _build_user_prompt(inp, repo)
+    prompt = _build_user_prompt(inp, repo, selected_files)
     schema = PlanAdapter.json_schema()
-
-    raw = llm.chat_with_schema(
+    raw = run_ctx.llm.chat_with_schema(
         prompt,
         {
             "type": "json_schema",
@@ -122,49 +170,115 @@ def _ensure_dict(raw):
     return raw
 
 
-def _build_user_prompt(inp: PlanInput, repo: RepoContext) -> str:
-    g = inp.gather
-    issue = g.issue_context
+MAX_FILE_LINES = 400
+MAX_TOTAL_FILE_CHARS = 60_000
+MIN_FILE_CONFIDENCE = 0.7
 
-    parts: list[str] = []
-    parts.append(f"# Issue {issue.issue_id}: {issue.title}")
-    parts.append("")
-    parts.append("## Description")
-    parts.append(issue.body.strip() or "(empty)")
-    parts.append("")
 
-    parts.append("## Acceptance criteria")
+def _numbered(path: Path) -> str:
+    try:
+        text = path.read_text(encoding="utf-8", errors="replace")
+    except OSError as e:
+        return f"(could not read {path}: {e})"
+
+    lines = text.splitlines()
+    if len(lines) <= MAX_FILE_LINES:
+        return "\n".join(f"{i:>4}  {l}" for i, l in enumerate(lines, 1))
+
+    head_n = MAX_FILE_LINES * 2 // 3
+    tail_n = MAX_FILE_LINES - head_n
+    head = lines[:head_n]
+    tail = lines[-tail_n:]
+    elided = len(lines) - head_n - tail_n
+    body = [f"{i:>4}  {l}" for i, l in enumerate(head, 1)]
+    body.append(f"      ... ({elided} lines elided) ...")
+    body += [f"{i:>4}  {l}" for i, l in enumerate(tail, len(lines) - tail_n + 1)]
+    return "\n".join(body)
+
+
+def _issue_block(issue) -> str:
+    out = [f"# Issue {issue.issue_id}: {issue.title}", "", "## Description",
+           issue.body.strip() or "(empty)", "", "## Acceptance criteria"]
     if issue.acceptance_criteria:
-        for i, ac in enumerate(issue.acceptance_criteria, 1):
-            parts.append(f"{i}. {ac}")
+        out += [f"{i}. {ac}" for i, ac in enumerate(issue.acceptance_criteria, 1)]
     else:
-        parts.append("(none stated)")
-    parts.append("")
+        out.append("(none stated)")
+    return "\n".join(out)
 
-    if issue.comments:
-        parts.append("## Prior comments")
-        for c in issue.comments:
-            parts.append(f"- [{c.created_at}] {c.author}: {c.body.strip()}")
-        parts.append("")
 
-    parts.append("## Feasibility verdict (already confirmed)")
-    parts.append(f"Verdict: feasible")
-    parts.append(f"Reasoning: {inp.feasibility.reasoning}")
-    parts.append(f"Confidence: {inp.feasibility.confidence}")
-    parts.append("")
+def _comments_block(comments) -> str:
+    lines = ["## Prior comments"]
+    lines += [f"- [{c.created_at}] {c.author}: {c.body.strip()}" for c in comments]
+    return "\n".join(lines)
 
-    parts.append("## Repository context")
-    parts.append(f"- url: {repo.remote_url}")
-    parts.append(f"- default branch: {repo.base_branch}")
-    parts.append("")
 
-    parts.append("## Linked files")
-    if g.linked_files:
-        for f in g.linked_files:
-            parts.append(f"- {f}")
-    else:
-        parts.append("(none)")
-    parts.append("")
+def _feasibility_block(f) -> str:
+    return "\n".join([
+        "## Feasibility verdict (already confirmed)",
+        f"Verdict: feasible",
+        f"Reasoning: {f.reasoning}",
+        f"Confidence: {f.confidence}",
+    ])
 
-    parts.append("Produce the plan. Return ONLY the JSON object.")
-    return "\n".join(parts)
+
+def _repo_block(repo) -> str:
+    return "\n".join([
+        "## Repository context",
+        f"- url: {repo.remote_url}",
+        f"- default branch: {repo.base_branch}",
+    ])
+
+
+def _files_block(repo, selected_files) -> str:
+    kept = [f for f in selected_files.selections if f.confidence >= MIN_FILE_CONFIDENCE]
+    kept.sort(key=lambda f: f.confidence, reverse=True)
+
+    lines = ["## Linked files"]
+    if not kept:
+        lines.append("(none selected above confidence threshold)")
+        return "\n".join(lines)
+
+    budget = MAX_TOTAL_FILE_CHARS
+    for f in kept:
+        if budget <= 0:
+            lines.append(f"- {f.path} (omitted: file budget exhausted)")
+            continue
+        content = _numbered(repo.repo_dir / f.path)
+        if len(content) > budget:
+            content = content[:budget] + "\n      ... (truncated) ..."
+        budget -= len(content)
+        lines += [
+            "",
+            f"### `{f.path}` (confidence {f.confidence:.2f})",
+            "```",
+            content,
+            "```",
+        ]
+    return "\n".join(lines)
+
+
+def _instructions_block() -> str:
+    return "\n".join([
+        "## Task",
+        "Produce an implementation plan for the issue above.",
+        "",
+        "Rules:",
+        "- Reference concrete file paths and line numbers from the linked files.",
+        "- Each step must be independently verifiable.",
+        "- Call out any assumptions you're making.",
+        "",
+        "Return ONLY the JSON object matching the plan schema. No prose, no markdown fence.",
+    ])
+
+
+def _build_user_prompt(inp, repo, selected_files) -> str:
+    g = inp.gather
+    blocks = [
+        _issue_block(g.issue_context),
+        _comments_block(g.issue_context.comments) if g.issue_context.comments else None,
+        _feasibility_block(inp.feasibility),
+        _repo_block(repo),
+        _files_block(repo, selected_files),
+        _instructions_block(),
+    ]
+    return "\n\n".join(b for b in blocks if b)

common/llm_client.py

@@ -1,12 +1,66 @@
+import hashlib
 import json
+import logging
+from pathlib import Path
+from typing import Optional, Type
+
 from openai import OpenAI
+from pydantic import BaseModel
+
+class NoSchema(BaseModel): ...
+
+
+logger = logging.getLogger("llm client")
+
+class ResponseCache:
+    """File-backed cache: prompt-hash -> validated-model JSON. Makes runs idempotent."""
+
+    def __init__(self, path: Optional[Path] = None) -> None:
+        self.path = path
+        self._mem: dict[str, str] = {}
+        if path and path.exists():
+            try:
+                self._mem = json.loads(path.read_text("utf-8"))
+            except Exception:  # noqa: BLE001
+                logger.warning("Corrupt cache at %s; starting fresh", path)
+
+    @staticmethod
+    def key(system: str, user: str, schema: Type[BaseModel]) -> str:
+        h = hashlib.sha256()
+        h.update(schema.__name__.encode())
+        h.update(b"\x00")
+        h.update(system.encode())
+        h.update(b"\x00")
+        h.update(user.encode())
+        return h.hexdigest()
+
+    def get(self, k: str) -> Optional[str]:
+        return self._mem.get(k)
+
+    def put(self, k: str, v: str) -> None:
+        self._mem[k] = v
+        if self.path:
+            self.path.parent.mkdir(parents=True, exist_ok=True)
+            tmp = self.path.with_suffix(self.path.suffix + ".tmp")
+            tmp.write_text(json.dumps(self._mem, indent=2, sort_keys=True), "utf-8")
+            tmp.replace(self.path)
+        else:
+            logger.warning("No path specified for cache!")
+
 
 class LLMClient:
-    def __init__(self, base_url, api_key: str | None = None, model: str = "gpt-4o-mini"):
+    def __init__(self, base_url, api_key: str | None = None, model: str = "gpt-4o-mini", cache: Optional[ResponseCache] = None):
         self.model = model
         self.client = OpenAI(base_url=base_url, api_key=api_key or "ollama")
+        self.cache = cache
 
     def chat_with_schema(self, prompt: str, schema: dict, system: str | None = None) -> str | None:
+        # --- idempotency: serve from cache when prompt+system+schema match ---
+
+        cache_key = ResponseCache.key(system or "", prompt, NoSchema) if self.cache else None
+        if cache_key and self.cache and (hit := self.cache.get(cache_key)) is not None:
+            return json.loads(hit).get('response', "")
+
         assert_strict_mode_clean(schema)
         kwargs = {
             "model": self.model,
@@ -19,6 +73,10 @@ class LLMClient:
             "response_format": schema,
         }
         resp = self.client.chat.completions.create(**kwargs)
+
+        if cache_key and self.cache:
+            self.cache.put(cache_key, json.dumps({"response": resp.choices[0].message.content or ""}))
+
         return resp.choices[0].message.content
 
     def chat(self, system: str, user: str, json_mode: bool = False, images: list[str] | None = None) -> str | None:

contracts/CodeLanguages.py

@@ -0,0 +1,24 @@
+from enum import Enum
+from typing import Literal
+
+
+class Language(str, Enum):
+    PYTHON = "python"
+    JAVASCRIPT = "javascript"
+    TYPESCRIPT = "typescript"
+    JAVA = "java"
+    GO = "go"
+    RUST = "rust"
+    CPP = "cpp"
+    C = "c"
+
+LanguageLiteral = Literal[
+    Language.PYTHON,
+    Language.JAVASCRIPT,
+    Language.TYPESCRIPT,
+    Language.JAVA,
+    Language.GO,
+    Language.RUST,
+    Language.CPP,
+    Language.C,
+]

contracts/GraphAnalyzer.py

@@ -0,0 +1,51 @@
+import pandas as pd
+from pydantic import BaseModel, Field, ConfigDict
+
+from contracts.RepoContext import Language
+
+
+class DependencyNode(BaseModel):
+    """A single node in the dependency graph."""
+    model_config = ConfigDict(frozen=True)
+    
+    id: str = Field(..., description="Unique identifier (file path or module name)")
+    label: str = Field(..., description="Human-readable label")
+    language: Language
+    is_external: bool = Field(
+        default=False,
+        description="True if the dependency is outside the repository",
+    )
+
+
+class DependencyEdge(BaseModel):
+    """A directed edge from source → target (source depends on target)."""
+    source: str = Field(..., description="Node id of the dependant")
+    target: str = Field(..., description="Node id of the dependency")
+    kind: str = Field(
+        default="import",
+        description="Edge kind: import, include, inherit, call, etc.",
+    )
+
+
+class DependencyGraph(BaseModel):
+    """Complete dependency graph result."""
+    root: str = Field(..., description="Entrypoint node id")
+    nodes: list[DependencyNode]
+    edges: list[DependencyEdge]
+    metadata: dict[str, str] = Field(default_factory=dict)
+
+
+class AnalyzeResult(BaseModel):
+    """Return shape of :func:`analyze`."""
+    model_config = ConfigDict(arbitrary_types_allowed=True)
+
+    df: pd.DataFrame
+    isolated: list[DependencyNode]
+    leaf_no_deps: list[DependencyNode]
+    entry_no_dependents: list[DependencyNode]
+    widely_used: list[tuple[DependencyNode, int]]
+    used_by_packages: dict[DependencyNode, int]
+    wccs: list[set[DependencyNode]]
+    sccs: list[set[DependencyNode]]
+    node2comm: dict[DependencyNode, int]
+    comms: list[set[DependencyNode]]

contracts/RepoContext.py

@@ -1,65 +1,40 @@
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from enum import Enum
 from pathlib import Path
-from typing import Optional, Literal, Any
+from typing import Optional, Literal, Any, Generic
 
-from pydantic import field_validator, BaseModel, Field
+import pandas as pd
+from pydantic import field_validator, BaseModel, Field, ConfigDict, field_serializer
+
+from contracts.CodeLanguages import Language
+from contracts.GraphAnalyzer import AnalyzeResult, DependencyGraph
 
 
-@dataclass(frozen=True)
+@dataclass
 class RepoContext:
-    url: str
-    default_branch: str
-    language_hint: str | None      # "python" | "typescript" | "go" | None
-
-class Language(str, Enum):
-    PYTHON = "python"
-    JAVASCRIPT = "javascript"
-    TYPESCRIPT = "typescript"
-    JAVA = "java"
-    GO = "go"
-    RUST = "rust"
-    CPP = "cpp"
-    C = "c"
-
-LanguageLiteral = Literal[
-    Language.PYTHON,
-    Language.JAVASCRIPT,
-    Language.TYPESCRIPT,
-    Language.JAVA,
-    Language.GO,
-    Language.RUST,
-    Language.CPP,
-    Language.C,
-]
-
-class DependencyNode(BaseModel):
-    """A single node in the dependency graph."""
-    id: str = Field(..., description="Unique identifier (file path or module name)")
-    label: str = Field(..., description="Human-readable label")
-    language: Language
-    is_external: bool = Field(
-        default=False,
-        description="True if the dependency is outside the repository",
-    )
+    """Result object carrying all info a coding agent needs."""
+    remote_url: str
+    branch: str
+    base_branch: str
+    head_commit: str
+    is_new_clone: bool
+    is_new_branch: bool
+    repo_dir: Path = Field(..., description="Absolute path to the cloned repository")
+    original_branch: Optional[str] = None
+    uncommitted_changes: Optional[str] = None  # git diff (tracked)
+    untracked_files: list[str] = field(default_factory=list)
+    stash_ref: Optional[str] = None
+    env: dict = field(default_factory=dict)
 
 
-class DependencyEdge(BaseModel):
-    """A directed edge from source → target (source depends on target)."""
-    source: str = Field(..., description="Node id of the dependant")
-    target: str = Field(..., description="Node id of the dependency")
-    kind: str = Field(
-        default="import",
-        description="Edge kind: import, include, inherit, call, etc.",
-    )
+    @field_validator("repo_path")
+    @classmethod
+    def repo_must_exist(cls, v: Path) -> Path:
+        if not v.is_dir():
+            raise ValueError(f"Repository path does not exist or is not a directory: {v}")
+        return v.resolve()
 
 
-class DependencyGraph(BaseModel):
-    """Complete dependency graph result."""
-    root: str = Field(..., description="Entrypoint node id")
-    nodes: list[DependencyNode]
-    edges: list[DependencyEdge]
-    metadata: dict[str, str] = Field(default_factory=dict)
 
 
 class ToolRequirement(BaseModel):
@@ -81,33 +56,21 @@ class AnalysisError(BaseModel):
 
 class AnalysisInput(BaseModel):
     """Input schema for the analyzer."""
-    repo_path: Path = Field(..., description="Absolute path to the cloned repository")
-    language: Language
-    entrypoint: str = Field(
-        ...,
-        description="Relative path from repo_path to the entrypoint file",
-    )
-
-    @field_validator("repo_path")
-    @classmethod
-    def repo_must_exist(cls, v: Path) -> Path:
-        if not v.is_dir():
-            raise ValueError(f"Repository path does not exist or is not a directory: {v}")
-        return v.resolve()
-
-    @field_validator("entrypoint")
-    @classmethod
-    def entrypoint_must_exist(cls, v: str, info) -> str:
-        repo = info.data.get("repo_path")
-        if repo and not (repo / v).is_file():
-            raise ValueError(f"Entrypoint not found: {repo / v}")
-        return v
+    repo: RepoContext
 
 
 class AnalysisResult(BaseModel):
     """Top-level result — either a graph or an error."""
+    model_config = ConfigDict(arbitrary_types_allowed=True)
+
     success: bool
     graph: Optional[DependencyGraph] = None
     error: Optional[AnalysisError] = None
-    leaf_clusters: Any
-    res_all: Any
+    leaf_clusters: Any = None
+    res_all: AnalyzeResult | None = None
+
+    @field_serializer("leaf_clusters")
+    def _ser_leaf_clusters(self, v: Any, _info):
+        if isinstance(v, pd.DataFrame):
+            return v.to_dict(orient="records")
+        return v  # already JSON-safe

contracts/coders/FileSelection.py

@@ -0,0 +1,16 @@
+from typing import Literal
+
+from pydantic import BaseModel, Field
+
+from contracts.base import _StrictModel
+
+
+class FileSelection(_StrictModel):
+    path: str = Field(...)
+    role: Literal["primary", "context", "test"] = Field(...)
+    reason: str = Field(...)
+    confidence: float = Field(ge=0.0, le=1.0)
+
+class FileSelectionOutput(_StrictModel):
+    selections: list[FileSelection] = Field(...)
+    notes: list[str] = Field(...)

contracts/coders/RunContext.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 import secrets
 from dataclasses import dataclass
 from datetime import datetime, timezone
+from pathlib import Path
 from typing import Any
 
 from agents.coders.state import AgentState
@@ -15,9 +16,13 @@ from common.youtrack_mcp_client import YouTrackMCPClient
 
 @dataclass(frozen=True)
 class AgentConfig:
+    agent_dir: Path
+
     # ── project-level ──────────────────────────────────────────
     youtrack_project: str
-    gitea_repo: str
+    git_name: str
+    git_email: str
+    gitea_repo: str = ""
     gitea_target_branch: str = "main"
 
     # ── limits (snapshotted into state at run start) ───────────
@@ -39,6 +44,13 @@ class AgentConfig:
     # ── language hints (for Plan) ──────────────────────────────
     language_markers: dict[str, list[str]] = None   # filled from project
 
+    def project_mem_dir(self):
+        p = self.agent_dir / "memory" / f"{self.youtrack_project}"
+        if not p.exists():
+            p.mkdir(parents=True, exist_ok=True)
+        return p
+
+
 
 @dataclass
 class RunContext: