@opencodehub/ingestion 0.1.0

package/dist/pipeline/phases/incremental-scope.js

@@ -0,0 +1,225 @@
+/**
+ * Incremental scope phase.
+ *
+ * Given a prior-run graph projection ({@link PreviousGraph}) and the current
+ * scan output, compute the **import closure** of files whose content hash
+ * changed since the last run. Downstream phases can consult this output to
+ * narrow their working set — today it is purely **passive**: the phase emits
+ * the closure and stats without modifying what crossFile / mro / communities
+ * / processes actually process. That's a deliberate v1.0 choice: wiring each
+ * downstream phase to honour the closure is invasive and risky for the first
+ * iteration. We keep the pipeline observably correct (full reindex always
+ * runs) while recording the *intended* savings so a followup can flip the
+ * active switch behind a feature flag.
+ *
+ * ## Algorithm
+ *
+ * 1. Read `options.incrementalFrom`. If absent, or if `options.force` is set,
+ *    emit `mode="full"` covering every scanned file. Bail early.
+ * 2. Walk the scan output and compute `changedFiles` = files whose
+ *    `contentSha` is unknown to the prior graph OR differs from it. For
+ *    content-hash comparison we treat a file that is present in both the
+ *    prior `files[]` and the current scan as "unchanged" only when the hash
+ *    actually matches. Prior-graph consumers (`analyze.ts`) supply the hash
+ *    by reading the persisted scan state; phases that need richer metadata
+ *    (e.g. `defines` edges) can extend {@link PreviousGraph} later without a
+ *    breaking change here.
+ * 3. BFS forward from `changedFiles` along IMPORTS edges to depth 2 (who
+ *    *uses* the changed files — "downstream" in consumer sense).
+ * 4. BFS backward from `changedFiles` along IMPORTS edges to depth 2 (what
+ *    the changed files *use* — "upstream" in producer sense).
+ * 5. Take one hop of heritage ancestors + descendants (EXTENDS / IMPLEMENTS)
+ *    for each changed file so subtype MROs refresh when a base class moves.
+ * 6. If the union exceeds 30% of the current total file count, fall back to
+ *    a full reindex (`mode="full"`, `fullReindexBecause="closure-too-large"`).
+ *    The safety valve prevents pathological "touched a universally-imported
+ *    utility" cases from running an incremental pass that ends up bigger
+ *    than a cold build.
+ *
+ * ## Determinism
+ *
+ * All emitted arrays (`changedFiles`, `closureFiles`) are sorted
+ * alphabetically. The BFS keeps its frontier sorted at every step; visited
+ * order has no effect on the final set, but sorting at emission time makes
+ * the logs reproducible across runs for the same input.
+ */
+import { SCAN_PHASE_NAME } from "./scan.js";
+/** Depth of the forward + backward IMPORTS BFS per the research spec. */
+const IMPORTS_BFS_DEPTH = 2;
+/** Safety valve threshold. Closure size ratios above this fall back to full. */
+const FULL_REINDEX_THRESHOLD = 0.3;
+export const INCREMENTAL_SCOPE_PHASE_NAME = "incremental-scope";
+export const incrementalScopePhase = {
+    name: INCREMENTAL_SCOPE_PHASE_NAME,
+    deps: [SCAN_PHASE_NAME],
+    async run(ctx, deps) {
+        const scan = deps.get(SCAN_PHASE_NAME);
+        if (scan === undefined) {
+            throw new Error("incremental-scope: scan output missing from dependency map");
+        }
+        const totalFiles = scan.files.length;
+        const allPaths = scan.files.map((f) => f.relPath);
+        // The scanned set is already deterministically sorted by `runScan`, but
+        // we re-sort defensively: incremental-scope must never trust a caller's
+        // ordering invariants for a hot-path output.
+        const allSorted = [...allPaths].sort();
+        const prior = ctx.options.incrementalFrom;
+        const force = ctx.options.force === true;
+        if (force) {
+            return {
+                mode: "full",
+                changedFiles: [],
+                closureFiles: allSorted,
+                fullReindexBecause: "force-flag",
+                totalFiles,
+                closureRatio: totalFiles === 0 ? 0 : 1,
+            };
+        }
+        if (prior === undefined) {
+            return {
+                mode: "full",
+                changedFiles: [],
+                closureFiles: allSorted,
+                fullReindexBecause: "no-prior-graph",
+                totalFiles,
+                closureRatio: totalFiles === 0 ? 0 : 1,
+            };
+        }
+        const changedFiles = computeChangedFiles(scan.files, prior);
+        if (changedFiles.length === 0) {
+            // No content drift: closure is empty. We still emit mode="incremental"
+            // so downstream phases can observe "nothing to do" without inferring
+            // it from an ambiguous full-mode marker.
+            return {
+                mode: "incremental",
+                changedFiles: [],
+                closureFiles: [],
+                totalFiles,
+                closureRatio: 0,
+            };
+        }
+        // ---- Build adjacency maps from the prior graph. --------------------
+        //
+        // `importForward` mirrors the on-graph direction (importer -> target);
+        // `importBackward` inverts it so we can walk "who imports me" in one
+        // step. Heritage is a single symmetric map because the closure wants
+        // both ancestors and descendants in one hop.
+        const importForward = new Map();
+        const importBackward = new Map();
+        for (const edge of prior.importEdges) {
+            pushIntoBucket(importForward, edge.importer, edge.target);
+            pushIntoBucket(importBackward, edge.target, edge.importer);
+        }
+        const heritage = new Map();
+        for (const edge of prior.heritageEdges) {
+            pushIntoBucket(heritage, edge.childFile, edge.parentFile);
+            pushIntoBucket(heritage, edge.parentFile, edge.childFile);
+        }
+        // Sort every adjacency list so BFS frontier order is a pure function
+        // of the input graph, regardless of edge insertion order.
+        for (const map of [importForward, importBackward, heritage]) {
+            for (const [k, v] of map) {
+                map.set(k, [...v].sort());
+            }
+        }
+        const closure = new Set(changedFiles);
+        bfsBounded(closure, importForward, changedFiles, IMPORTS_BFS_DEPTH);
+        bfsBounded(closure, importBackward, changedFiles, IMPORTS_BFS_DEPTH);
+        // Heritage is a single-hop expansion per the research algorithm.
+        for (const f of changedFiles) {
+            const neighbours = heritage.get(f);
+            if (neighbours === undefined)
+                continue;
+            for (const n of neighbours)
+                closure.add(n);
+        }
+        // Prune closure to files that still exist in the current scan — a file
+        // deleted between runs should not propagate into a re-analysis target.
+        const currentSet = new Set(allPaths);
+        const pruned = [...closure].filter((f) => currentSet.has(f)).sort();
+        const ratio = totalFiles === 0 ? 0 : pruned.length / totalFiles;
+        if (ratio > FULL_REINDEX_THRESHOLD) {
+            ctx.onProgress?.({
+                phase: INCREMENTAL_SCOPE_PHASE_NAME,
+                kind: "note",
+                message: `incremental-scope: closure ${pruned.length}/${totalFiles} ` +
+                    `(${(ratio * 100).toFixed(1)}%) exceeds ${FULL_REINDEX_THRESHOLD * 100}% threshold — ` +
+                    `falling back to full reindex`,
+            });
+            return {
+                mode: "full",
+                changedFiles: [...changedFiles].sort(),
+                closureFiles: allSorted,
+                fullReindexBecause: "closure-too-large",
+                totalFiles,
+                closureRatio: ratio,
+            };
+        }
+        return {
+            mode: "incremental",
+            changedFiles: [...changedFiles].sort(),
+            closureFiles: pruned,
+            totalFiles,
+            closureRatio: ratio,
+        };
+    },
+};
+/**
+ * Compute the set of files whose content hash differs from the prior graph.
+ *
+ * Semantics:
+ *  - File present in both and hash matches → unchanged.
+ *  - File present in both and hash differs → changed.
+ *  - File only in current scan (newly added) → changed.
+ *  - File only in prior graph (deleted) → ignored (cannot re-process what
+ *    no longer exists; downstream phases must detect deletions through the
+ *    upsert pipeline instead).
+ */
+function computeChangedFiles(current, prior) {
+    const priorHashByPath = new Map();
+    for (const f of prior.files)
+        priorHashByPath.set(f.relPath, f.contentSha);
+    const changed = [];
+    for (const f of current) {
+        const priorHash = priorHashByPath.get(f.relPath);
+        if (priorHash === undefined || priorHash !== f.sha256) {
+            changed.push(f.relPath);
+        }
+    }
+    return changed.sort();
+}
+/**
+ * Breadth-first walk capped at `maxDepth` hops. `closure` accumulates the
+ * visited set; starting seeds are assumed to already live in `closure`.
+ *
+ * The frontier is re-sorted at every depth so BFS visitation order is a
+ * deterministic function of the graph, not of Map iteration order.
+ */
+function bfsBounded(closure, adj, seeds, maxDepth) {
+    let frontier = [...seeds].sort();
+    for (let depth = 0; depth < maxDepth && frontier.length > 0; depth += 1) {
+        const nextFrontier = [];
+        for (const node of frontier) {
+            const neighbours = adj.get(node);
+            if (neighbours === undefined)
+                continue;
+            for (const n of neighbours) {
+                if (!closure.has(n)) {
+                    closure.add(n);
+                    nextFrontier.push(n);
+                }
+            }
+        }
+        nextFrontier.sort();
+        frontier = nextFrontier;
+    }
+}
+function pushIntoBucket(m, key, value) {
+    const existing = m.get(key);
+    if (existing === undefined) {
+        m.set(key, [value]);
+        return;
+    }
+    existing.push(value);
+}
+//# sourceMappingURL=incremental-scope.js.map

package/dist/pipeline/phases/incremental-scope.js.map

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package/dist/pipeline/phases/markdown.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Markdown phase — projects prose documents onto the graph.
+ *
+ * Consumes the structure phase output (for its pathSet) and scans every file
+ * whose extension matches `.md`, `.mdx`, or `.markdown`. For each such file
+ * the phase:
+ *   1. Emits a `Section` node per H1..H6 heading.
+ *   2. Links sections to their owning file via CONTAINS (top-level sections)
+ *      and to each other along the heading hierarchy (parent → child).
+ *   3. Scans the body for `[text](./path.md)` or `[text](./path.md#anchor)`
+ *      style internal links and emits REFERENCES edges from the containing
+ *      section (falling back to the file when no section encloses the link)
+ *      to the target file — but only if the target path resolves against the
+ *      structure phase pathSet.
+ *
+ * Determinism: input files are iterated in the sorted relPath order supplied
+ * by the scan phase, headings are processed in source order, and link target
+ * resolution is deterministic given the pathSet.
+ *
+ * No new dependencies — heading and link parsing is done with compiled regex.
+ */
+import type { PipelinePhase } from "../types.js";
+export interface MarkdownOutput {
+    readonly sectionCount: number;
+    readonly linkCount: number;
+}
+export declare const MARKDOWN_PHASE_NAME = "markdown";
+export declare const markdownPhase: PipelinePhase<MarkdownOutput>;
+//# sourceMappingURL=markdown.d.ts.map

package/dist/pipeline/phases/markdown.d.ts.map

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package/dist/pipeline/phases/markdown.js

@@ -0,0 +1,298 @@
+/**
+ * Markdown phase — projects prose documents onto the graph.
+ *
+ * Consumes the structure phase output (for its pathSet) and scans every file
+ * whose extension matches `.md`, `.mdx`, or `.markdown`. For each such file
+ * the phase:
+ *   1. Emits a `Section` node per H1..H6 heading.
+ *   2. Links sections to their owning file via CONTAINS (top-level sections)
+ *      and to each other along the heading hierarchy (parent → child).
+ *   3. Scans the body for `[text](./path.md)` or `[text](./path.md#anchor)`
+ *      style internal links and emits REFERENCES edges from the containing
+ *      section (falling back to the file when no section encloses the link)
+ *      to the target file — but only if the target path resolves against the
+ *      structure phase pathSet.
+ *
+ * Determinism: input files are iterated in the sorted relPath order supplied
+ * by the scan phase, headings are processed in source order, and link target
+ * resolution is deterministic given the pathSet.
+ *
+ * No new dependencies — heading and link parsing is done with compiled regex.
+ */
+import { promises as fs } from "node:fs";
+import path from "node:path";
+import { makeNodeId } from "@opencodehub/core-types";
+import { SCAN_PHASE_NAME } from "./scan.js";
+import { STRUCTURE_PHASE_NAME } from "./structure.js";
+/** File extensions treated as markdown. Lowercase, leading dot. */
+const MARKDOWN_EXTS = new Set([".md", ".mdx", ".markdown"]);
+/** Match ATX-style headings `#`-`######` followed by the heading text. */
+const HEADING_RE = /^(#{1,6})\s+(.+?)\s*#*\s*$/;
+/** Match `[anchor](target)` links. Captures only the target. */
+const LINK_RE = /\[(?:[^\]]*)\]\(([^)\s]+)(?:\s+"[^"]*")?\)/g;
+export const MARKDOWN_PHASE_NAME = "markdown";
+export const markdownPhase = {
+    name: MARKDOWN_PHASE_NAME,
+    deps: [STRUCTURE_PHASE_NAME],
+    async run(ctx, deps) {
+        const structure = deps.get(STRUCTURE_PHASE_NAME);
+        if (structure === undefined) {
+            throw new Error("markdown: structure output missing from dependency map");
+        }
+        // markdown reads the scan output indirectly via phaseOutputs — it is not
+        // declared as a direct dep (structure already consumes it and we prefer
+        // a single declared dep chain) but the full phaseOutputs map is visible.
+        const scan = ctx.phaseOutputs.get(SCAN_PHASE_NAME);
+        if (scan === undefined) {
+            throw new Error("markdown: scan output missing from phase outputs");
+        }
+        return runMarkdown(ctx, scan, structure);
+    },
+};
+async function runMarkdown(ctx, scan, structure) {
+    const markdownFiles = scan.files.filter((f) => MARKDOWN_EXTS.has(extOf(f.relPath)));
+    let sectionCount = 0;
+    let linkCount = 0;
+    for (const file of markdownFiles) {
+        let content;
+        try {
+            const buf = await fs.readFile(file.absPath);
+            content = buf.toString("utf8");
+        }
+        catch (err) {
+            ctx.onProgress?.({
+                phase: MARKDOWN_PHASE_NAME,
+                kind: "warn",
+                message: `markdown: cannot read ${file.relPath}: ${err.message}`,
+            });
+            continue;
+        }
+        const headings = parseHeadings(content);
+        const sectionsOnFile = emitSectionsAndContains(ctx, file, headings);
+        sectionCount += sectionsOnFile.length;
+        linkCount += emitReferenceLinks(ctx, file, content, sectionsOnFile, structure.pathSet);
+    }
+    return { sectionCount, linkCount };
+}
+function parseHeadings(content) {
+    const out = [];
+    let lineNum = 1;
+    let lineStart = 0;
+    let inFence = false;
+    const len = content.length;
+    for (let i = 0; i <= len; i += 1) {
+        const ch = i === len ? "\n" : content.charAt(i);
+        if (ch === "\n") {
+            const line = content.slice(lineStart, i);
+            const trimmed = line.trimEnd();
+            // Toggle code-fence state on lines starting with ``` or ~~~.
+            if (/^(?:```|~~~)/.test(trimmed)) {
+                inFence = !inFence;
+            }
+            else if (!inFence) {
+                const m = HEADING_RE.exec(trimmed);
+                if (m !== null) {
+                    const hashes = m[1];
+                    const text = m[2];
+                    if (hashes !== undefined && text !== undefined) {
+                        const level = hashes.length;
+                        const cleaned = text.trim();
+                        if (cleaned.length > 0) {
+                            out.push({ level, text: cleaned, line: lineNum, offset: lineStart });
+                        }
+                    }
+                }
+            }
+            lineStart = i + 1;
+            lineNum += 1;
+        }
+    }
+    return out;
+}
+function emitSectionsAndContains(ctx, file, headings) {
+    const fileId = makeNodeId("File", file.relPath, file.relPath);
+    // Guarantee the File node exists even if structure was skipped. addNode
+    // is idempotent on repeat calls.
+    const fileNode = {
+        id: fileId,
+        kind: "File",
+        name: basename(file.relPath),
+        filePath: file.relPath,
+        ...(file.language !== undefined ? { language: file.language } : {}),
+        contentHash: file.sha256,
+    };
+    ctx.graph.addNode(fileNode);
+    // Track the chain of currently-open sections by level so each new heading
+    // can find its parent and produce a stable qualified key.
+    const stack = [];
+    const bindings = [];
+    for (const h of headings) {
+        while (stack.length > 0 &&
+            stack[stack.length - 1].heading.level >= h.level) {
+            stack.pop();
+        }
+        const parent = stack.length > 0 ? stack[stack.length - 1] : undefined;
+        const parentHeadingText = parent?.heading.text ?? "";
+        const id = makeNodeId("Section", file.relPath, `${parentHeadingText}/${h.text}`, {
+            parameterCount: h.level,
+        });
+        const node = {
+            id,
+            kind: "Section",
+            name: h.text,
+            filePath: file.relPath,
+            level: h.level,
+            startLine: h.line,
+        };
+        ctx.graph.addNode(node);
+        const binding = {
+            heading: h,
+            id,
+            bodyStart: h.offset,
+            bodyEnd: Number.POSITIVE_INFINITY,
+        };
+        bindings.push(binding);
+        if (parent === undefined) {
+            ctx.graph.addEdge({
+                from: fileId,
+                to: id,
+                type: "CONTAINS",
+                confidence: 1,
+                reason: "file-to-section",
+            });
+        }
+        else {
+            ctx.graph.addEdge({
+                from: parent.id,
+                to: id,
+                type: "CONTAINS",
+                confidence: 1,
+                reason: "section-to-subsection",
+            });
+        }
+        stack.push(binding);
+    }
+    // Close body offsets: each section body ends where the next heading of
+    // equal-or-lower level starts.
+    for (let i = 0; i < bindings.length; i += 1) {
+        const current = bindings[i];
+        for (let j = i + 1; j < bindings.length; j += 1) {
+            const next = bindings[j];
+            if (next.heading.level <= current.heading.level) {
+                current.bodyEnd = next.heading.offset;
+                break;
+            }
+        }
+    }
+    return bindings;
+}
+function emitReferenceLinks(ctx, file, content, sections, pathSet) {
+    const fileId = makeNodeId("File", file.relPath, file.relPath);
+    const importerDir = parentDir(file.relPath);
+    let linkCount = 0;
+    LINK_RE.lastIndex = 0;
+    let match = LINK_RE.exec(content);
+    while (match !== null) {
+        const target = match[1];
+        const matchIdx = match.index;
+        match = LINK_RE.exec(content);
+        if (target === undefined)
+            continue;
+        // Drop external links, anchors-only, or obviously non-file URIs.
+        if (/^[a-z][a-z0-9+.-]*:/i.test(target))
+            continue;
+        if (target.startsWith("#"))
+            continue;
+        if (target.startsWith("mailto:"))
+            continue;
+        // Separate anchor from path.
+        const hashIdx = target.indexOf("#");
+        const rawPath = hashIdx === -1 ? target : target.slice(0, hashIdx);
+        if (rawPath.length === 0)
+            continue;
+        const resolved = resolveLinkTarget(rawPath, importerDir, pathSet);
+        if (resolved === undefined)
+            continue;
+        const targetId = makeNodeId("File", resolved, resolved);
+        const ownerId = ownerSectionFor(sections, matchIdx) ?? fileId;
+        ctx.graph.addEdge({
+            from: ownerId,
+            to: targetId,
+            type: "REFERENCES",
+            confidence: 0.8,
+            reason: "markdown-link",
+        });
+        linkCount += 1;
+    }
+    return linkCount;
+}
+function ownerSectionFor(sections, offset) {
+    // Pick the deepest section whose body bracket contains `offset`.
+    let best;
+    for (const s of sections) {
+        if (offset >= s.bodyStart && offset < s.bodyEnd) {
+            if (best === undefined || s.heading.level > best.heading.level) {
+                best = s;
+            }
+        }
+    }
+    return best?.id;
+}
+function resolveLinkTarget(rawPath, importerDir, pathSet) {
+    // Decode percent-escapes and strip leading `./`.
+    let p = rawPath;
+    try {
+        p = decodeURIComponent(p);
+    }
+    catch {
+        // leave raw path in place if it's not valid percent-encoded
+    }
+    if (p.startsWith("/")) {
+        const candidate = p.slice(1);
+        return pathSet.has(candidate) ? candidate : undefined;
+    }
+    const joined = posixJoin(importerDir, p);
+    const normalized = normalizePath(joined);
+    if (pathSet.has(normalized))
+        return normalized;
+    return undefined;
+}
+function extOf(relPath) {
+    const e = path.extname(relPath);
+    return e.toLowerCase();
+}
+function basename(p) {
+    const idx = p.lastIndexOf("/");
+    if (idx < 0)
+        return p;
+    return p.slice(idx + 1);
+}
+function parentDir(p) {
+    const idx = p.lastIndexOf("/");
+    if (idx <= 0)
+        return "";
+    return p.slice(0, idx);
+}
+function posixJoin(dir, rel) {
+    if (dir === "")
+        return rel;
+    if (rel === "")
+        return dir;
+    return `${dir}/${rel}`;
+}
+function normalizePath(p) {
+    const parts = p.split("/");
+    const out = [];
+    for (const part of parts) {
+        if (part === "" || part === ".")
+            continue;
+        if (part === "..") {
+            if (out.length > 0)
+                out.pop();
+            continue;
+        }
+        out.push(part);
+    }
+    return out.join("/");
+}
+//# sourceMappingURL=markdown.js.map

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package/dist/pipeline/phases/mro.d.ts

@@ -0,0 +1,24 @@
+/**
+ * MRO phase — emit `METHOD_OVERRIDES` / `METHOD_IMPLEMENTS` edges by
+ * linearising each class's ancestor chain with its language-specific
+ * strategy.
+ *
+ * Strategy-per-language table:
+ *  - `python` → `c3` (raises on ambiguity; caught + skipped per-class).
+ *  - `typescript`, `tsx`, `javascript`, `rust` → `first-wins`.
+ *  - `java`, `csharp` → `single-inheritance`; interfaces drive
+ *    `METHOD_IMPLEMENTS` edges separately.
+ *  - `go` → `none`; no class-based inheritance. Skipped entirely.
+ *
+ * Determinism: parents and methods are iterated in sorted-id order, so the
+ * edge set is byte-identical across runs.
+ */
+import type { PipelinePhase } from "../types.js";
+export declare const MRO_PHASE_NAME = "mro";
+export interface MroOutput {
+    readonly overridesCount: number;
+    readonly implementsCount: number;
+    readonly conflictCount: number;
+}
+export declare const mroPhase: PipelinePhase<MroOutput>;
+//# sourceMappingURL=mro.d.ts.map

package/dist/pipeline/phases/mro.d.ts.map

@@ -0,0 +1 @@
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