Git Internals

A working map of what's actually happening under .git/ — objects, refs, the index, pack files, and the merge/rebase machinery built on top of them. Most sections below end with a quick knowledge check; track your progress as you go:

1. Object Model

Git stores everything as content-addressed objects in .git/objects/. Four types:

Content-addressed: SHA = sha1(type + space + size + \0 + content). Same content = same SHA always.

SHA-1: 40 hex chars (160-bit). Legacy, still default.
SHA-256: 64 hex chars (256-bit). Enable with: git init --object-format=sha256

Storage: .git/objects/ab/cdef1234... — first 2 chars = directory, rest = filename.

# Inspect any object
git cat-file -t <sha>      # type
git cat-file -p <sha>      # pretty-print content

# Example:
git cat-file -p HEAD       # shows commit object
git cat-file -p HEAD^{tree} # shows root tree
git ls-tree HEAD            # list tree entries

2. Working Tree → Index → Local Repo → Remote

flowchart LR
    WT["Working Tree<br/>your files on disk"]
    IDX["Index / Staging<br/>.git/index"]
    LOCAL["Local Repo<br/>.git/objects"]
    REMOTE["Remote<br/>GitHub/GitLab"]

    WT -->|git add| IDX
    IDX -->|git commit| LOCAL
    LOCAL -->|git push| REMOTE
    REMOTE -->|git fetch| LOCAL
    LOCAL -->|git checkout| WT
    LOCAL -->|git merge/rebase| WT
    IDX -->|git restore --staged| WT

3. Refs

Refs are files in .git/refs/ containing a SHA (or another ref for symbolic refs).

HEAD is a symbolic ref: ref: refs/heads/main. In detached state it contains a raw SHA.

Lightweight tag: just a ref pointing to a commit SHA. No object created.
Annotated tag: creates a tag object (has tagger, message, signature). Points to commit.

git tag v1.0              # lightweight
git tag -a v1.0 -m "msg"  # annotated (creates tag object)
git cat-file -t v1.0      # "commit" vs "tag"

4. Pack Files

Loose objects: one file per object. Fine for small repos.
Pack files: Git bundles objects together for efficiency.

git gc                          → pack loose objects
git gc --aggressive             → more compression
git count-objects -v            → see loose vs packed counts

Pack format:

• .git/objects/pack/pack-<sha>.pack — the objects (delta-compressed)
• .git/objects/pack/pack-<sha>.idx — index for fast lookup by SHA

Delta compression: similar objects stored as base + delta. A file's history stores diffs, not full copies. Git stores the newest version as the base and older versions as deltas (reverse delta).

git verify-pack -v .git/objects/pack/pack-*.idx | sort -k3 -n | tail -10
# Shows largest objects in pack by size

5. Index (Staging Area) Internals

The index is a binary file at .git/index. It is a snapshot of the working tree ready for the next commit.

Each entry contains:

• file mode, UID/GID, file size, mtime
• SHA of the blob
• file path (relative to repo root)
• flags (merge stage: 0=normal, 1/2/3=conflict stages)

git ls-files --stage          # dump index entries
git ls-files -u               # show conflict (unmerged) entries

During a merge conflict, the index holds 3 stages for conflicted files:

• Stage 1: common ancestor (base)
• Stage 2: ours (HEAD)
• Stage 3: theirs (MERGE_HEAD)

6. Merge vs Rebase Internals

3-Way Merge

Git finds the merge base (common ancestor commit), then applies changes from both branches:

merge base = git merge-base branch1 branch2

If the same lines changed in both → conflict. Git writes conflict markers to the working tree.

Fast-forward merge: when no divergence exists (one branch is an ancestor of the other). HEAD pointer just moves forward. No merge commit created.

git merge --ff-only feature   # fail if not fast-forwardable
git merge --no-ff feature     # always create merge commit

Rebase Internals

Rebase replays commits one by one onto a new base:

graph LR
    subgraph Before["Before: git rebase main"]
        A1["A"] --> B1["B (main)"]
        A1 --> C1["C"] --> D1["D (feature)"]
    end
    subgraph After["After: git rebase main"]
        A2["A"] --> B2["B (main)"] --> C2["C' (new SHA)"] --> D2["D' (new SHA, feature)"]
    end

Step by step:

1. git merge-base feature main → finds A (common ancestor)
2. Extract patches: C-diff, D-diff
3. git reset --hard main → move feature to B
4. Apply C-diff → creates C' (new SHA, different parent = different hash)
5. Apply D-diff → creates D' (new SHA)

Conflict during rebase:

git rebase main
# CONFLICT (content): Merge conflict in src/handler.go
# Fix conflict in editor, then:
git add src/handler.go
git rebase --continue   # applies next commit
# OR:
git rebase --skip       # skip this commit entirely
# OR:
git rebase --abort      # abandon, restore original branch

Interactive rebase — rewrite history before pushing:

git rebase -i HEAD~4   # last 4 commits
# Editor opens showing:
# pick a1b2c3 add feature X
# pick d4e5f6 fix typo
# pick g7h8i9 wip
# pick j0k1l2 final cleanup
#
# Commands: pick, squash (s), fixup (f), reword (r), edit (e), drop (d)
# Squash d4e5f6 into a1b2c3:
# pick a1b2c3 add feature X
# squash d4e5f6 fix typo     ← merged into previous, keeps both messages
# fixup g7h8i9 wip           ← merged into previous, discards this message
# reword j0k1l2 final cleanup ← prompts to edit message

--onto — transplant commits to a different base:

# Move commits that are on feature but NOT on bugfix, onto main
git rebase --onto main bugfix feature
# Before: main ← bugfix ← feature
# After:  main ← feature' (bugfix commits dropped)
# Use case: feature was accidentally branched from bugfix, not main

Key rule: git rebase rewrites SHAs. Never rebase commits that have been pushed to a shared remote branch — it will require force push and break everyone else's history.

7. Reflog

The reflog records every movement of a ref (HEAD, branches). It is local only and expires after 90 days by default.

git reflog                    # HEAD reflog
git reflog show main          # main branch reflog
git reflog --all              # all refs

Recover Deleted Branch

# 1. Find the SHA of the deleted branch tip
git reflog | grep "branch-name"
# or: git log --walk-reflogs --oneline

# 2. Recreate the branch
git checkout -b branch-name <sha>
# or: git branch branch-name <sha>

Recover Deleted Commits (reset --hard undo)

git reflog                    # find SHA before reset
git reset --hard <sha>        # restore HEAD to that point
# or: git checkout -b recovery <sha>

Object DAG & Commit Graph

graph TD
    subgraph Objects
        C2["commit: abc123<br/>msg: add feature"]
        C1["commit: def456<br/>msg: initial"]
        T2["tree: 789...<br/>root dir"]
        T1["tree: 012...<br/>root dir"]
        B1["blob: hello.go<br/>v2 content"]
        B0["blob: hello.go<br/>v1 content"]
        B2["blob: main.go<br/>content"]
    end

    C2 -->|parent| C1
    C2 -->|tree| T2
    C1 -->|tree| T1
    T2 -->|hello.go| B1
    T2 -->|main.go| B2
    T1 -->|hello.go| B0
    T1 -->|main.go| B2

gitGraph
   commit id: "A"
   commit id: "B"
   branch feature
   commit id: "C"
   commit id: "D"
   checkout main
   commit id: "E"
   merge feature id: "M" type: HIGHLIGHT