*fix(nix): resolve nix profile conflicts without numeric indices and fix update pkgmgr system test*

* Switch conflict handling from index-based removal to token-based removal (*nix profile remove <name>*) for newer nix versions
* Add robust parsing of *nix profile list --json* with normalization and heuristics for output/name matching
* Detect at runtime whether numeric profile indices are supported and fall back automatically when they are not
* Ensure *pkgmgr* / *package-manager* flake outputs are correctly identified and cleaned up during reinstall
* Fix failing E2E test *test_update_pkgmgr_shallow_pkgmgr_with_system* by reliably removing conflicting profile entries before reinstall

https://chatgpt.com/share/693efae5-b8bc-800f-94e3-28c93b74ed7b

src/pkgmgr/actions/install/installers/nix/conflicts.py

@@ -0,0 +1,100 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, List
+
+from .profile import NixProfileInspector
+from .retry import GitHubRateLimitRetry
+from .runner import CommandRunner
+from .textparse import NixConflictTextParser
+
+if TYPE_CHECKING:
+    from pkgmgr.actions.install.context import RepoContext
+
+
+class NixConflictResolver:
+    """
+    Resolves nix profile file conflicts by:
+      1. Parsing conflicting store paths from stderr
+      2. Mapping them to profile remove tokens via `nix profile list --json`
+      3. Removing those tokens deterministically
+      4. Retrying install
+    """
+
+    def __init__(
+        self,
+        runner: CommandRunner,
+        retry: GitHubRateLimitRetry,
+        profile: NixProfileInspector,
+    ) -> None:
+        self._runner = runner
+        self._retry = retry
+        self._profile = profile
+        self._parser = NixConflictTextParser()
+
+    def resolve(
+        self,
+        ctx: "RepoContext",
+        install_cmd: str,
+        stdout: str,
+        stderr: str,
+        *,
+        output: str,
+        max_rounds: int = 10,
+    ) -> bool:
+        quiet = bool(getattr(ctx, "quiet", False))
+        combined = f"{stdout}\n{stderr}"
+
+        for _ in range(max_rounds):
+            # 1) Extract conflicting store prefixes from nix error output
+            store_prefixes = self._parser.existing_store_prefixes(combined)
+
+            # 2) Resolve them to concrete remove tokens
+            tokens: List[str] = self._profile.find_remove_tokens_for_store_prefixes(
+                ctx,
+                self._runner,
+                store_prefixes,
+            )
+
+            # 3) Fallback: output-name based lookup (also covers nix suggesting: `nix profile remove pkgmgr`)
+            if not tokens:
+                tokens = self._profile.find_remove_tokens_for_output(ctx, self._runner, output)
+
+            if tokens:
+                if not quiet:
+                    print(
+                        "[nix] conflict detected; removing existing profile entries: "
+                        + ", ".join(tokens)
+                    )
+
+                for t in tokens:
+                    # tokens may contain things like "pkgmgr" or "pkgmgr-1" or quoted tokens (we keep raw)
+                    self._runner.run(ctx, f"nix profile remove {t}", allow_failure=True)
+
+                res = self._retry.run_with_retry(ctx, self._runner, install_cmd)
+                if res.returncode == 0:
+                    return True
+
+                combined = f"{res.stdout}\n{res.stderr}"
+                continue
+
+            # 4) Last-resort fallback: use textual remove tokens from stderr (“nix profile remove X”)
+            tokens = self._parser.remove_tokens(combined)
+            if tokens:
+                if not quiet:
+                    print("[nix] fallback remove tokens: " + ", ".join(tokens))
+
+                for t in tokens:
+                    self._runner.run(ctx, f"nix profile remove {t}", allow_failure=True)
+
+                res = self._retry.run_with_retry(ctx, self._runner, install_cmd)
+                if res.returncode == 0:
+                    return True
+
+                combined = f"{res.stdout}\n{res.stderr}"
+                continue
+
+            if not quiet:
+                print("[nix] conflict detected but could not resolve profile entries to remove.")
+            return False
+
+        return False

src/pkgmgr/actions/install/installers/nix/installer.py

@@ -1,12 +1,12 @@
-# src/pkgmgr/actions/install/installers/nix/installer.py
 from __future__ import annotations
 
 import os
 import shutil
-from typing import List, Tuple, TYPE_CHECKING
+from typing import TYPE_CHECKING, List, Tuple
 
 from pkgmgr.actions.install.installers.base import BaseInstaller
 
+from .conflicts import NixConflictResolver
 from .profile import NixProfileInspector
 from .retry import GitHubRateLimitRetry, RetryPolicy
 from .runner import CommandRunner
@@ -14,6 +14,7 @@ from .runner import CommandRunner
 if TYPE_CHECKING:
     from pkgmgr.actions.install.context import RepoContext
 
+
 class NixFlakeInstaller(BaseInstaller):
     layer = "nix"
     FLAKE_FILE = "flake.nix"
@@ -22,15 +23,18 @@ class NixFlakeInstaller(BaseInstaller):
         self._runner = CommandRunner()
         self._retry = GitHubRateLimitRetry(policy=policy)
         self._profile = NixProfileInspector()
+        self._conflicts = NixConflictResolver(self._runner, self._retry, self._profile)
 
-    # ------------------------------------------------------------------ #
-    # Compatibility: supports()
-    # ------------------------------------------------------------------ #
+        # Newer nix rejects numeric indices; we learn this at runtime and cache the decision.
+        self._indices_supported: bool | None = None
 
     def supports(self, ctx: "RepoContext") -> bool:
         if os.environ.get("PKGMGR_DISABLE_NIX_FLAKE_INSTALLER") == "1":
             if not ctx.quiet:
-                print("[INFO] PKGMGR_DISABLE_NIX_FLAKE_INSTALLER=1 – skipping NixFlakeInstaller.")
+                print(
+                    "[INFO] PKGMGR_DISABLE_NIX_FLAKE_INSTALLER=1 – "
+                    "skipping NixFlakeInstaller."
+                )
             return False
 
         if shutil.which("nix") is None:
@@ -38,20 +42,12 @@ class NixFlakeInstaller(BaseInstaller):
 
         return os.path.exists(os.path.join(ctx.repo_dir, self.FLAKE_FILE))
 
-    # ------------------------------------------------------------------ #
-    # Compatibility: output selection
-    # ------------------------------------------------------------------ #
-
     def _profile_outputs(self, ctx: "RepoContext") -> List[Tuple[str, bool]]:
         # (output_name, allow_failure)
         if ctx.identifier in {"pkgmgr", "package-manager"}:
             return [("pkgmgr", False), ("default", True)]
         return [("default", False)]
 
-    # ------------------------------------------------------------------ #
-    # Compatibility: run()
-    # ------------------------------------------------------------------ #
-
     def run(self, ctx: "RepoContext") -> None:
         if not self.supports(ctx):
             return
@@ -59,11 +55,12 @@ class NixFlakeInstaller(BaseInstaller):
         outputs = self._profile_outputs(ctx)
 
         if not ctx.quiet:
-            print(
+            msg = (
                 "[nix] flake detected in "
                 f"{ctx.identifier}, ensuring outputs: "
                 + ", ".join(name for name, _ in outputs)
             )
+            print(msg)
 
         for output, allow_failure in outputs:
             if ctx.force_update:
@@ -71,13 +68,13 @@ class NixFlakeInstaller(BaseInstaller):
             else:
                 self._install_only(ctx, output, allow_failure)
 
-    # ------------------------------------------------------------------ #
-    # Core logic (unchanged semantics)
-    # ------------------------------------------------------------------ #
-
     def _installable(self, ctx: "RepoContext", output: str) -> str:
         return f"{ctx.repo_dir}#{output}"
 
+    # ---------------------------------------------------------------------
+    # Core install path
+    # ---------------------------------------------------------------------
+
     def _install_only(self, ctx: "RepoContext", output: str, allow_failure: bool) -> None:
         install_cmd = f"nix profile install {self._installable(ctx, output)}"
 
@@ -85,35 +82,56 @@ class NixFlakeInstaller(BaseInstaller):
             print(f"[nix] install: {install_cmd}")
 
         res = self._retry.run_with_retry(ctx, self._runner, install_cmd)
-
         if res.returncode == 0:
             if not ctx.quiet:
                 print(f"[nix] output '{output}' successfully installed.")
             return
 
+        # Conflict resolver first (handles the common “existing package already provides file” case)
+        if self._conflicts.resolve(
+            ctx,
+            install_cmd,
+            res.stdout,
+            res.stderr,
+            output=output,
+        ):
+            if not ctx.quiet:
+                print(f"[nix] output '{output}' successfully installed after conflict cleanup.")
+            return
+
         if not ctx.quiet:
             print(
                 f"[nix] install failed for '{output}' (exit {res.returncode}), "
-                "trying index-based upgrade/remove+install..."
+                "trying upgrade/remove+install..."
             )
 
-        indices = self._profile.find_installed_indices_for_output(ctx, self._runner, output)
+        # If indices are supported, try legacy index-upgrade path.
+        if self._indices_supported is not False:
+            indices = self._profile.find_installed_indices_for_output(ctx, self._runner, output)
 
-        upgraded = False
-        for idx in indices:
-            if self._upgrade_index(ctx, idx):
-                upgraded = True
-                if not ctx.quiet:
-                    print(f"[nix] output '{output}' successfully upgraded (index {idx}).")
+            upgraded = False
+            for idx in indices:
+                if self._upgrade_index(ctx, idx):
+                    upgraded = True
+                    if not ctx.quiet:
+                        print(f"[nix] output '{output}' successfully upgraded (index {idx}).")
 
-        if upgraded:
-            return
+            if upgraded:
+                return
 
-        if indices and not ctx.quiet:
-            print(f"[nix] upgrade failed; removing indices {indices} and reinstalling '{output}'.")
+            if indices and not ctx.quiet:
+                print(f"[nix] upgrade failed; removing indices {indices} and reinstalling '{output}'.")
 
-        for idx in indices:
-            self._remove_index(ctx, idx)
+            for idx in indices:
+                self._remove_index(ctx, idx)
+
+            # If we learned indices are unsupported, immediately fall back below
+            if self._indices_supported is False:
+                self._remove_tokens_for_output(ctx, output)
+
+        else:
+            # indices explicitly unsupported
+            self._remove_tokens_for_output(ctx, output)
 
         final = self._runner.run(ctx, install_cmd, allow_failure=True)
         if final.returncode == 0:
@@ -122,17 +140,24 @@ class NixFlakeInstaller(BaseInstaller):
             return
 
         print(f"[ERROR] Failed to install Nix flake output '{output}' (exit {final.returncode})")
-
         if not allow_failure:
             raise SystemExit(final.returncode)
 
         print(f"[WARNING] Continuing despite failure of optional output '{output}'.")
 
-    # ------------------------------------------------------------------ #
-    # force_update path (unchanged semantics)
-    # ------------------------------------------------------------------ #
+    # ---------------------------------------------------------------------
+    # force_update path
+    # ---------------------------------------------------------------------
 
     def _force_upgrade_output(self, ctx: "RepoContext", output: str, allow_failure: bool) -> None:
+        # Prefer token path if indices unsupported (new nix)
+        if self._indices_supported is False:
+            self._remove_tokens_for_output(ctx, output)
+            self._install_only(ctx, output, allow_failure)
+            if not ctx.quiet:
+                print(f"[nix] output '{output}' successfully upgraded.")
+            return
+
         indices = self._profile.find_installed_indices_for_output(ctx, self._runner, output)
 
         upgraded_any = False
@@ -143,7 +168,8 @@ class NixFlakeInstaller(BaseInstaller):
                     print(f"[nix] output '{output}' successfully upgraded (index {idx}).")
 
         if upgraded_any:
-            print(f"[nix] output '{output}' successfully upgraded.")
+            if not ctx.quiet:
+                print(f"[nix] output '{output}' successfully upgraded.")
             return
 
         if indices and not ctx.quiet:
@@ -152,17 +178,52 @@ class NixFlakeInstaller(BaseInstaller):
         for idx in indices:
             self._remove_index(ctx, idx)
 
+        # If we learned indices are unsupported, also remove by token to actually clear conflicts
+        if self._indices_supported is False:
+            self._remove_tokens_for_output(ctx, output)
+
         self._install_only(ctx, output, allow_failure)
 
-        print(f"[nix] output '{output}' successfully upgraded.")
+        if not ctx.quiet:
+            print(f"[nix] output '{output}' successfully upgraded.")
 
-    # ------------------------------------------------------------------ #
+    # ---------------------------------------------------------------------
     # Helpers
-    # ------------------------------------------------------------------ #
+    # ---------------------------------------------------------------------
+
+    def _stderr_says_indices_unsupported(self, stderr: str) -> bool:
+        s = (stderr or "").lower()
+        return "no longer supports indices" in s or "does not support indices" in s
 
     def _upgrade_index(self, ctx: "RepoContext", idx: int) -> bool:
-        res = self._runner.run(ctx, f"nix profile upgrade --refresh {idx}", allow_failure=True)
+        cmd = f"nix profile upgrade --refresh {idx}"
+        res = self._runner.run(ctx, cmd, allow_failure=True)
+
+        if self._stderr_says_indices_unsupported(getattr(res, "stderr", "")):
+            self._indices_supported = False
+            return False
+
+        if self._indices_supported is None:
+            self._indices_supported = True
+
         return res.returncode == 0
 
     def _remove_index(self, ctx: "RepoContext", idx: int) -> None:
-        self._runner.run(ctx, f"nix profile remove {idx}", allow_failure=True)
+        res = self._runner.run(ctx, f"nix profile remove {idx}", allow_failure=True)
+
+        if self._stderr_says_indices_unsupported(getattr(res, "stderr", "")):
+            self._indices_supported = False
+
+        if self._indices_supported is None:
+            self._indices_supported = True
+
+    def _remove_tokens_for_output(self, ctx: "RepoContext", output: str) -> None:
+        tokens = self._profile.find_remove_tokens_for_output(ctx, self._runner, output)
+        if not tokens:
+            return
+
+        if not ctx.quiet:
+            print(f"[nix] indices unsupported; removing by token(s): {', '.join(tokens)}")
+
+        for t in tokens:
+            self._runner.run(ctx, f"nix profile remove {t}", allow_failure=True)

src/pkgmgr/actions/install/installers/nix/profile.py

@@ -1,71 +0,0 @@
-from __future__ import annotations
-
-import json
-from typing import Any, List, TYPE_CHECKING
-
-
-if TYPE_CHECKING:
-    from pkgmgr.actions.install.context import RepoContext
-    from .runner import CommandRunner
- 
-class NixProfileInspector:
-    """
-    Reads and interprets `nix profile list --json` and provides helpers for
-    finding indices matching a given output name.
-    """
-
-    def find_installed_indices_for_output(self, ctx: "RepoContext", runner: "CommandRunner", output: str) -> List[int]:
-        res = runner.run(ctx, "nix profile list --json", allow_failure=True)
-        if res.returncode != 0:
-            return []
-
-        try:
-            data = json.loads(res.stdout or "{}")
-        except json.JSONDecodeError:
-            return []
-
-        indices: List[int] = []
-
-        elements = data.get("elements")
-        if isinstance(elements, dict):
-            for idx_str, elem in elements.items():
-                try:
-                    idx = int(idx_str)
-                except (TypeError, ValueError):
-                    continue
-                if self._element_matches_output(elem, output):
-                    indices.append(idx)
-            return sorted(indices)
-
-        if isinstance(elements, list):
-            for elem in elements:
-                idx = elem.get("index") if isinstance(elem, dict) else None
-                if isinstance(idx, int) and self._element_matches_output(elem, output):
-                    indices.append(idx)
-            return sorted(indices)
-
-        return []
-
-    @staticmethod
-    def element_matches_output(elem: Any, output: str) -> bool:
-        return NixProfileInspector._element_matches_output(elem, output)
-
-    @staticmethod
-    def _element_matches_output(elem: Any, output: str) -> bool:
-        out = (output or "").strip()
-        if not out or not isinstance(elem, dict):
-            return False
-
-        candidates: List[str] = []
-        for k in ("attrPath", "originalUrl", "url", "storePath", "name"):
-            v = elem.get(k)
-            if isinstance(v, str) and v:
-                candidates.append(v)
-
-        for c in candidates:
-            if c == out:
-                return True
-            if f"#{out}" in c:
-                return True
-
-        return False

src/pkgmgr/actions/install/installers/nix/profile/__init__.py

@@ -0,0 +1,4 @@
+from .inspector import NixProfileInspector
+from .models import NixProfileEntry
+
+__all__ = ["NixProfileInspector", "NixProfileEntry"]

src/pkgmgr/actions/install/installers/nix/profile/inspector.py

@@ -0,0 +1,162 @@
+from __future__ import annotations
+
+from typing import Any, List, TYPE_CHECKING
+
+from .matcher import (
+    entry_matches_output,
+    entry_matches_store_path,
+    stable_unique_ints,
+)
+from .normalizer import normalize_elements
+from .parser import parse_profile_list_json
+from .result import extract_stdout_text
+
+if TYPE_CHECKING:
+    # Keep these as TYPE_CHECKING-only to avoid runtime import cycles.
+    from pkgmgr.actions.install.context import RepoContext
+    from pkgmgr.core.command.runner import CommandRunner
+
+
+class NixProfileInspector:
+    """
+    Reads and inspects the user's Nix profile list (JSON).
+
+    Public API:
+      - list_json()
+      - find_installed_indices_for_output()   (legacy; may not work on newer nix)
+      - find_indices_by_store_path()          (legacy; may not work on newer nix)
+      - find_remove_tokens_for_output()
+      - find_remove_tokens_for_store_prefixes()
+    """
+
+    def list_json(self, ctx: "RepoContext", runner: "CommandRunner") -> dict[str, Any]:
+        res = runner.run(ctx, "nix profile list --json", allow_failure=False)
+        raw = extract_stdout_text(res)
+        return parse_profile_list_json(raw)
+
+    # ---------------------------------------------------------------------
+    # Legacy index helpers (still useful on older nix; newer nix may reject indices)
+    # ---------------------------------------------------------------------
+
+    def find_installed_indices_for_output(
+        self,
+        ctx: "RepoContext",
+        runner: "CommandRunner",
+        output: str,
+    ) -> List[int]:
+        data = self.list_json(ctx, runner)
+        entries = normalize_elements(data)
+
+        hits: List[int] = []
+        for e in entries:
+            if e.index is None:
+                continue
+            if entry_matches_output(e, output):
+                hits.append(e.index)
+
+        return stable_unique_ints(hits)
+
+    def find_indices_by_store_path(
+        self,
+        ctx: "RepoContext",
+        runner: "CommandRunner",
+        store_path: str,
+    ) -> List[int]:
+        needle = (store_path or "").strip()
+        if not needle:
+            return []
+
+        data = self.list_json(ctx, runner)
+        entries = normalize_elements(data)
+
+        hits: List[int] = []
+        for e in entries:
+            if e.index is None:
+                continue
+            if entry_matches_store_path(e, needle):
+                hits.append(e.index)
+
+        return stable_unique_ints(hits)
+
+    # ---------------------------------------------------------------------
+    # New token-based helpers (works with newer nix where indices are rejected)
+    # ---------------------------------------------------------------------
+
+    def find_remove_tokens_for_output(
+        self,
+        ctx: "RepoContext",
+        runner: "CommandRunner",
+        output: str,
+    ) -> List[str]:
+        """
+        Returns profile remove tokens to remove entries matching a given output.
+
+        We always include the raw output token first because nix itself suggests:
+          nix profile remove pkgmgr
+        """
+        out = (output or "").strip()
+        if not out:
+            return []
+
+        data = self.list_json(ctx, runner)
+        entries = normalize_elements(data)
+
+        tokens: List[str] = [out]  # critical: matches nix's own suggestion for conflicts
+
+        for e in entries:
+            if entry_matches_output(e, out):
+                # Prefer removing by key/name (non-index) when possible.
+                # New nix rejects numeric indices; these tokens are safer.
+                k = (e.key or "").strip()
+                n = (e.name or "").strip()
+
+                if k and not k.isdigit():
+                    tokens.append(k)
+                elif n and not n.isdigit():
+                    tokens.append(n)
+
+        # stable unique preserving order
+        seen: set[str] = set()
+        uniq: List[str] = []
+        for t in tokens:
+            if t and t not in seen:
+                uniq.append(t)
+                seen.add(t)
+        return uniq
+
+    def find_remove_tokens_for_store_prefixes(
+        self,
+        ctx: "RepoContext",
+        runner: "CommandRunner",
+        prefixes: List[str],
+    ) -> List[str]:
+        """
+        Returns remove tokens for entries whose store path matches any prefix.
+        """
+        prefixes = [(p or "").strip() for p in (prefixes or []) if p]
+        prefixes = [p for p in prefixes if p]
+        if not prefixes:
+            return []
+
+        data = self.list_json(ctx, runner)
+        entries = normalize_elements(data)
+
+        tokens: List[str] = []
+        for e in entries:
+            if not e.store_paths:
+                continue
+            if any(sp == p for sp in e.store_paths for p in prefixes):
+                k = (e.key or "").strip()
+                n = (e.name or "").strip()
+                if k and not k.isdigit():
+                    tokens.append(k)
+                elif n and not n.isdigit():
+                    tokens.append(n)
+
+        seen: set[str] = set()
+        uniq: List[str] = []
+        for t in tokens:
+            if t and t not in seen:
+                uniq.append(t)
+                seen.add(t)
+        return uniq

src/pkgmgr/actions/install/installers/nix/profile/matcher.py

@@ -0,0 +1,62 @@
+from __future__ import annotations
+
+from typing import List
+
+from .models import NixProfileEntry
+
+
+def entry_matches_output(entry: NixProfileEntry, output: str) -> bool:
+    """
+    Heuristic matcher: output is typically a flake output name (e.g. "pkgmgr"),
+    and we match against name/attrPath patterns.
+    """
+    out = (output or "").strip()
+    if not out:
+        return False
+
+    candidates = [entry.name, entry.attr_path]
+
+    for c in candidates:
+        c = (c or "").strip()
+        if not c:
+            continue
+
+        # Direct match
+        if c == out:
+            return True
+
+        # AttrPath contains "#<output>"
+        if f"#{out}" in c:
+            return True
+
+        # AttrPath ends with ".<output>"
+        if c.endswith(f".{out}"):
+            return True
+
+        # Name pattern "<output>-<n>" (common, e.g. pkgmgr-1)
+        if c.startswith(f"{out}-"):
+            return True
+
+        # Historical special case: repo is "package-manager" but output is "pkgmgr"
+        if out == "pkgmgr" and c.startswith("package-manager-"):
+            return True
+
+    return False
+
+
+def entry_matches_store_path(entry: NixProfileEntry, store_path: str) -> bool:
+    needle = (store_path or "").strip()
+    if not needle:
+        return False
+    return any((p or "") == needle for p in entry.store_paths)
+
+
+def stable_unique_ints(values: List[int]) -> List[int]:
+    seen: set[int] = set()
+    uniq: List[int] = []
+    for v in values:
+        if v in seen:
+            continue
+        uniq.append(v)
+        seen.add(v)
+    return uniq

src/pkgmgr/actions/install/installers/nix/profile/models.py

@@ -0,0 +1,17 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import List, Optional
+
+
+@dataclass(frozen=True)
+class NixProfileEntry:
+    """
+    Minimal normalized representation of one nix profile element entry.
+    """
+
+    key: str
+    index: Optional[int]
+    name: str
+    attr_path: str
+    store_paths: List[str]

src/pkgmgr/actions/install/installers/nix/profile/normalizer.py

@@ -0,0 +1,128 @@
+from __future__ import annotations
+
+import re
+from typing import Any, Dict, Iterable, List, Optional
+
+from .models import NixProfileEntry
+
+
+def coerce_index(key: str, entry: Dict[str, Any]) -> Optional[int]:
+    """
+    Nix JSON schema varies:
+      - elements keys might be "0", "1", ...
+      - or might be names like "pkgmgr-1"
+    Some versions include an explicit index field.
+    We try safe options in order.
+    """
+    k = (key or "").strip()
+
+    # 1) Classic: numeric keys
+    if k.isdigit():
+        try:
+            return int(k)
+        except Exception:
+            return None
+
+    # 2) Explicit index fields (schema-dependent)
+    for field in ("index", "id", "position"):
+        v = entry.get(field)
+        if isinstance(v, int):
+            return v
+        if isinstance(v, str) and v.strip().isdigit():
+            try:
+                return int(v.strip())
+            except Exception:
+                pass
+
+    # 3) Last resort: extract trailing number from key if it looks like "<name>-<n>"
+    m = re.match(r"^.+-(\d+)$", k)
+    if m:
+        try:
+            return int(m.group(1))
+        except Exception:
+            return None
+
+    return None
+
+
+def iter_store_paths(entry: Dict[str, Any]) -> Iterable[str]:
+    """
+    Yield all possible store paths from a nix profile JSON entry.
+
+    Nix has had schema shifts. We support common variants:
+      - "storePaths": ["/nix/store/..", ...]
+      - "storePaths": "/nix/store/.."  (rare)
+      - "storePath": "/nix/store/.."   (some variants)
+      - nested "outputs" dict(s) with store paths (best-effort)
+    """
+    if not isinstance(entry, dict):
+        return
+
+    sp = entry.get("storePaths")
+    if isinstance(sp, list):
+        for p in sp:
+            if isinstance(p, str):
+                yield p
+    elif isinstance(sp, str):
+        yield sp
+
+    sp2 = entry.get("storePath")
+    if isinstance(sp2, str):
+        yield sp2
+
+    outs = entry.get("outputs")
+    if isinstance(outs, dict):
+        for _, ov in outs.items():
+            if isinstance(ov, dict):
+                p = ov.get("storePath")
+                if isinstance(p, str):
+                    yield p
+
+
+def normalize_store_path(store_path: str) -> str:
+    """
+    Normalize store path for matching.
+    Currently just strips whitespace; hook for future normalization if needed.
+    """
+    return (store_path or "").strip()
+
+
+def normalize_elements(data: Dict[str, Any]) -> List[NixProfileEntry]:
+    """
+    Converts nix profile list JSON into a list of normalized entries.
+
+    JSON formats observed:
+      - {"elements": {"0": {...}, "1": {...}}}
+      - {"elements": {"pkgmgr-1": {...}, "pkgmgr-2": {...}}}
+    """
+    elements = data.get("elements")
+    if not isinstance(elements, dict):
+        return []
+
+    normalized: List[NixProfileEntry] = []
+
+    for k, entry in elements.items():
+        if not isinstance(entry, dict):
+            continue
+
+        idx = coerce_index(str(k), entry)
+        name = str(entry.get("name", "") or "")
+        attr = str(entry.get("attrPath", "") or "")
+
+        store_paths: List[str] = []
+        for p in iter_store_paths(entry):
+            sp = normalize_store_path(p)
+            if sp:
+                store_paths.append(sp)
+
+        normalized.append(
+            NixProfileEntry(
+                key=str(k),
+                index=idx,
+                name=name,
+                attr_path=attr,
+                store_paths=store_paths,
+            )
+        )
+
+    return normalized

src/pkgmgr/actions/install/installers/nix/profile/parser.py

@@ -0,0 +1,19 @@
+from __future__ import annotations
+
+import json
+from typing import Any, Dict
+
+
+def parse_profile_list_json(raw: str) -> Dict[str, Any]:
+    """
+    Parse JSON output from `nix profile list --json`.
+
+    Raises SystemExit with a helpful excerpt on parse failure.
+    """
+    try:
+        return json.loads(raw)
+    except json.JSONDecodeError as e:
+        excerpt = (raw or "")[:5000]
+        raise SystemExit(
+            f"[nix] Failed to parse `nix profile list --json`: {e}\n{excerpt}"
+        ) from e

src/pkgmgr/actions/install/installers/nix/profile/result.py

@@ -0,0 +1,28 @@
+from __future__ import annotations
+
+from typing import Any
+
+
+def extract_stdout_text(result: Any) -> str:
+    """
+    Normalize different runner return types to a stdout string.
+
+    Supported patterns:
+      - result is str -> returned as-is
+      - result is bytes/bytearray -> decoded UTF-8 (replace errors)
+      - result has `.stdout` (str or bytes) -> used
+      - fallback: str(result)
+    """
+    if isinstance(result, str):
+        return result
+
+    if isinstance(result, (bytes, bytearray)):
+        return bytes(result).decode("utf-8", errors="replace")
+
+    stdout = getattr(result, "stdout", None)
+    if isinstance(stdout, str):
+        return stdout
+    if isinstance(stdout, (bytes, bytearray)):
+        return bytes(stdout).decode("utf-8", errors="replace")
+
+    return str(result)

src/pkgmgr/actions/install/installers/nix/profile_list.py

@@ -0,0 +1,69 @@
+from __future__ import annotations
+
+import re
+from typing import TYPE_CHECKING, List, Tuple
+
+from .runner import CommandRunner
+
+if TYPE_CHECKING:
+    from pkgmgr.actions.install.context import RepoContext
+
+
+class NixProfileListReader:
+    def __init__(self, runner: CommandRunner) -> None:
+        self._runner = runner
+
+    @staticmethod
+    def _store_prefix(path: str) -> str:
+        raw = (path or "").strip()
+        m = re.match(r"^(/nix/store/[0-9a-z]{32}-[^/ \t]+)", raw)
+        return m.group(1) if m else raw
+
+    def entries(self, ctx: "RepoContext") -> List[Tuple[int, str]]:
+        res = self._runner.run(ctx, "nix profile list", allow_failure=True)
+        if res.returncode != 0:
+            return []
+
+        entries: List[Tuple[int, str]] = []
+        pat = re.compile(
+            r"^\s*(\d+)\s+.*?(/nix/store/[0-9a-z]{32}-[^/ \t]+)",
+            re.MULTILINE,
+        )
+
+        for m in pat.finditer(res.stdout or ""):
+            idx_s = m.group(1)
+            sp = m.group(2)
+            try:
+                idx = int(idx_s)
+            except Exception:
+                continue
+            entries.append((idx, self._store_prefix(sp)))
+
+        seen: set[int] = set()
+        uniq: List[Tuple[int, str]] = []
+        for idx, sp in entries:
+            if idx not in seen:
+                seen.add(idx)
+                uniq.append((idx, sp))
+
+        return uniq
+
+    def indices_matching_store_prefixes(self, ctx: "RepoContext", prefixes: List[str]) -> List[int]:
+        prefixes = [self._store_prefix(p) for p in prefixes if p]
+        prefixes = [p for p in prefixes if p]
+        if not prefixes:
+            return []
+
+        hits: List[int] = []
+        for idx, sp in self.entries(ctx):
+            if any(sp == p for p in prefixes):
+                hits.append(idx)
+
+        seen: set[int] = set()
+        uniq: List[int] = []
+        for i in hits:
+            if i not in seen:
+                seen.add(i)
+                uniq.append(i)
+
+        return uniq

src/pkgmgr/actions/install/installers/nix/textparse.py

@@ -0,0 +1,76 @@
+from __future__ import annotations
+
+import re
+from typing import List
+
+
+class NixConflictTextParser:
+    @staticmethod
+    def _store_prefix(path: str) -> str:
+        raw = (path or "").strip()
+        m = re.match(r"^(/nix/store/[0-9a-z]{32}-[^/ \t]+)", raw)
+        return m.group(1) if m else raw
+
+    def remove_tokens(self, text: str) -> List[str]:
+        pat = re.compile(
+            r"^\s*nix profile remove\s+([^\s'\"`]+|'[^']+'|\"[^\"]+\")\s*$",
+            re.MULTILINE,
+        )
+
+        tokens: List[str] = []
+        for m in pat.finditer(text or ""):
+            t = (m.group(1) or "").strip()
+            if (t.startswith("'") and t.endswith("'")) or (t.startswith('"') and t.endswith('"')):
+                t = t[1:-1]
+            if t:
+                tokens.append(t)
+
+        seen: set[str] = set()
+        uniq: List[str] = []
+        for t in tokens:
+            if t not in seen:
+                seen.add(t)
+                uniq.append(t)
+
+        return uniq
+
+    def existing_store_prefixes(self, text: str) -> List[str]:
+        lines = (text or "").splitlines()
+        prefixes: List[str] = []
+
+        in_existing = False
+        in_new = False
+
+        store_pat = re.compile(r"^\s*(/nix/store/[0-9a-z]{32}-[^ \t]+)")
+
+        for raw in lines:
+            line = raw.strip()
+
+            if "An existing package already provides the following file" in line:
+                in_existing = True
+                in_new = False
+                continue
+
+            if "This is the conflicting file from the new package" in line:
+                in_existing = False
+                in_new = True
+                continue
+
+            if in_existing:
+                m = store_pat.match(raw)
+                if m:
+                    prefixes.append(m.group(1))
+                    continue
+
+            _ = in_new
+
+        norm = [self._store_prefix(p) for p in prefixes if p]
+
+        seen: set[str] = set()
+        uniq: List[str] = []
+        for p in norm:
+            if p and p not in seen:
+                seen.add(p)
+                uniq.append(p)
+
+        return uniq

tests/integration/test_nix_profile_list_json.py

@@ -0,0 +1,63 @@
+from __future__ import annotations
+
+import json
+import unittest
+from dataclasses import dataclass
+
+
+@dataclass
+class FakeRunResult:
+    """
+    Mimics your runner returning a structured result object.
+    """
+    returncode: int
+    stdout: str
+    stderr: str = ""
+
+
+class FakeRunner:
+    """
+    Minimal runner stub: returns exactly what we configure.
+    """
+    def __init__(self, result):
+        self._result = result
+
+    def run(self, ctx, cmd: str, allow_failure: bool = False):
+        return self._result
+
+
+class TestE2ENixProfileListJsonParsing(unittest.TestCase):
+    """
+    This test verifies that NixProfileInspector can parse `nix profile list --json`
+    regardless of whether the CommandRunner returns:
+      - raw stdout string, OR
+      - a RunResult-like object with a `.stdout` attribute.
+    """
+
+    def test_list_json_accepts_raw_string(self) -> None:
+        from pkgmgr.actions.install.installers.nix.profile import NixProfileInspector
+
+        payload = {"elements": {"pkgmgr-1": {"attrPath": "packages.x86_64-linux.pkgmgr"}}}
+        raw = json.dumps(payload)
+
+        runner = FakeRunner(raw)
+        inspector = NixProfileInspector()
+
+        data = inspector.list_json(ctx=None, runner=runner)
+        self.assertEqual(data["elements"]["pkgmgr-1"]["attrPath"], "packages.x86_64-linux.pkgmgr")
+
+    def test_list_json_accepts_runresult_object(self) -> None:
+        from pkgmgr.actions.install.installers.nix.profile import NixProfileInspector
+
+        payload = {"elements": {"pkgmgr-1": {"attrPath": "packages.x86_64-linux.pkgmgr"}}}
+        raw = json.dumps(payload)
+
+        runner = FakeRunner(FakeRunResult(returncode=0, stdout=raw))
+        inspector = NixProfileInspector()
+
+        data = inspector.list_json(ctx=None, runner=runner)
+        self.assertEqual(data["elements"]["pkgmgr-1"]["attrPath"], "packages.x86_64-linux.pkgmgr")
+
+
+if __name__ == "__main__":
+    unittest.main()